scRNA-tools

A

alevinQC

Generate QC reports summarizing the output from an alevin run
Platform: R
Code: https://github.com/csoneson/alevinQC
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License: MIT
Categories: Interactive, Visualisation
Added: 2019-05-31, Updated: 2019-05-31

AltAnalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses.

Publications: 2, Preprints: 1, Total citations: 516

Publications
"Single-cell analysis of mixed-lineage states leading to a binary cell fate choice"
DOI: 10.1038/nature19348, Published: 2016-08-31, Citations: 459
"cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes"
DOI: 10.1093/nar/gkz789, Published: 2019-09-16, Citations: 54
Preprints
"cellHarmony: Cell-level matching and holistic comparison of single-cell transcriptomes"
DOI: 10.1101/412080, Citations: 3

Platform: Python
Code: https://github.com/nsalomonis/altanalyze
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License: Apache-2.0
Categories: Alternative Splicing, Cell Cycle, Classification, Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Networks, Gene Sets, Interactive, Marker Genes, Normalisation, Quantification, Visualisation
Added: 2017-07-16, Updated: 2018-11-12

ASAP

ASAP : Automated Single-cell Analysis Pipeline

Publications: 2, Preprints: 1, Total citations: 131

Publications
"ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data"
DOI: 10.1093/bioinformatics/btx337, Published: 2017-05-24, Citations: 106
"ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses"
DOI: 10.1093/nar/gkaa412, Published: 2020-05-25, Citations: 20
Preprints
"ASAP: A web-based platform for the analysis and interactive visualization of single-cell RNA-seq data"
DOI: 10.1101/096222, Citations: 5

Platform: R/Python
Code: https://github.com/DeplanckeLab/ASAP
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License: GPL-3.0
Categories: Clustering, Differential Expression, Gene Filtering, Interactive, Normalisation, Visualisation
Added: 2018-11-12, Updated: 2023-12-22

Asc-Seurat

Analytical single-cell Seurat-based web application

Publications: 1, Preprints: 1, Total citations: 42

Publications
"Asc-Seurat: analytical single-cell Seurat-based web application"
DOI: 10.1186/s12859-021-04472-2, Published: 2021-11-18, Citations: 37
Preprints
"Asc-Seurat – Analytical single-cell Seurat-based web application"
DOI: 10.1101/2021.03.19.436196, Citations: 5

Platform: R
Code: https://github.com/KirstLab/asc_seurat
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License: GPL-3.0
Categories: Clustering, Differential Expression, Dimensionality Reduction, Integration, Interactive, Ordering, Quality Control, Visualisation
Added: 2021-03-26, Updated: 2021-11-27

AUCell

AUCell is an R-package to analyze the state of gene-sets in single-cell RNA-seq data (i.e. identify cells with active gene signatures).

Publications: 1, Preprints: 1, Total citations: 3978

Publications
"SCENIC: single-cell regulatory network inference and clustering"
DOI: 10.1038/nmeth.4463, Published: 2017-10-09, Citations: 3963
Preprints
"SCENIC: Single-cell regulatory network inference and clustering"
DOI: 10.1101/144501, Citations: 15

Platform: R
Code: https://github.com/aertslab/AUCell
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last commitUnknown
License: Custom
Categories: Gene Networks, Interactive, Visualisation
Added: 2017-06-26, Updated: 2018-05-13

B

BingleSeq

A user-friendly R package for Bulk and Single-cell RNA-Seq data analyses

Publications: 1, Preprints: 1, Total citations: 11

Publications
"BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis"
DOI: 10.7717/peerj.10469, Published: 2020-12-22, Citations: 10
Preprints
"BingleSeq: A user-friendly R package for Bulk and Single-cell RNA-Seq Data Analysis"
DOI: 10.1101/2020.06.16.148239, Citations: 1

Platform: R
Code: https://github.com/dbdimitrov/BingleSeq
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last commitUnknown
License: MIT
Categories: Clustering, Differential Expression, Gene Sets, Interactive, Normalisation, Quality Control, Visualisation
Added: 2020-06-26, Updated: 2020-06-26

C

CancerInSilico

The CancerInSilico package provides an R interface for running mathematical models of tumor progresson.

Publications: 1, Preprints: 1, Total citations: 3

Publications
"CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer"
DOI: 10.1371/journal.pcbi.1006935, Published: 2019-04-19, Citations: 3
Preprints
"CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer"
DOI: 10.1101/328807, Citations: 0

Platform: R/C++
Code: https://github.com/FertigLab/CancerInSilico
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License: GPL-2.0
Categories: Cell Cycle, Gene Networks, Interactive, Simulation, Visualisation
Added: 2018-06-19, Updated: 2018-06-19

Cellar

Cell Type Annotation Robot

Publications: 1, Preprints: 1, Total citations: 21

Publications
"Interactive single-cell data analysis using Cellar"
DOI: 10.1038/s41467-022-29744-0, Published: 2022-04-14, Citations: 18
Preprints
"Cellar: Interactive single cell data annotation tool"
DOI: 10.1101/2021.03.19.436162, Citations: 3

Platform: Python/R
Code: https://github.com/euxhenh/cellar
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last commitUnknown
License: MIT
Categories: Classification, Clustering, Differential Expression, Dimensionality Reduction, Interactive, Quality Control
Added: 2021-03-26, Updated: 2022-04-30

cellBrowser

Python pipeline and Javascript scatter plot library for single-cell datasets
Platform: Python
Code: https://github.com/maximilianh/cellBrowser
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License: GPL-3.0
Categories: Interactive, Visualisation
Added: 2018-10-02, Updated: 2018-10-02

cellenium

Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data

Publications: 1, Preprints: 0, Total citations: 0

Publications
"Cellenium—a scalable and interactive visual analytics app for exploring multimodal single-cell data"
DOI: 10.1093/bioinformatics/btad349, Published: 2023-06-01, Citations: 0

Platform: TypeScript/Python
Code: https://github.com/Bayer-Group/cellenium
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last commitUnknown
License: MIT
Categories: Interactive, Visualisation
Added: 2023-07-01, Updated: 2023-07-01

CellexalVR

A feature-rich, fully interactive virtual reality environment for the visualisation and analysis of single-cell experiments

Publications: 1, Preprints: 1, Total citations: 31

Publications
"CellexalVR: A virtual reality platform to visualize and analyze single-cell omics data"
DOI: 10.1016/j.isci.2021.103251, Published: 2021-11, Citations: 20
Preprints
"CellexalVR: A virtual reality platform to visualise and analyse single-cell data"
DOI: 10.1101/329102, Citations: 11

Platform: Csharp
Code: https://github.com/sonejilab/cellexalvr
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License: GPL-3.0
Categories: Interactive, Visualisation
Added: 2020-10-05, Updated: 2021-11-27

CellMap

The CellMap is a RNA landscape inference method based on the graph Hodge decomposition
Platform: Python
Code: https://github.com/yusuke-imoto-lab/CellMap
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Categories: Dimensionality Reduction, Interactive, Visualisation
Added: 2023-03-31, Updated: 2023-03-31

CellRanger

Cell Ranger is a set of analysis pipelines that process Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

Publications: 1, Preprints: 1, Total citations: 5184

Publications
"Massively parallel digital transcriptional profiling of single cells"
DOI: 10.1038/ncomms14049, Published: 2017-01-16, Citations: 5159
Preprints
"Massively parallel digital transcriptional profiling of single cells"
DOI: 10.1101/065912, Citations: 25

Platform: Python/R
Code: https://github.com/10XGenomics/cellranger
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Categories: Alignment, Clustering, Differential Expression, Dimensionality Reduction, Interactive, Marker Genes, Quality Control, Quantification, UMIs, Visualisation
Added: 2017-06-08, Updated: 2018-04-09

CellTrek

CellTrek is a computational framework that can directly map single cells back to their spatial coordinates in tissue sections based on scRNA-seq and ST data

Publications: 1, Preprints: 1, Total citations: 130

Publications
"Spatial charting of single-cell transcriptomes in tissues"
DOI: 10.1038/s41587-022-01233-1, Published: 2022-03-21, Citations: 127
Preprints
"Spatial charting of single cell transcriptomes in tissues"
DOI: 10.1101/2021.11.24.469915, Citations: 3

Platform: R
Code: https://github.com/navinlabcode/CellTrek
starsN/A
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Categories: Integration, Interactive, Visualisation
Added: 2021-11-27, Updated: 2022-04-30

CellView

A ShinyApp to visualize and explore single cell datasets

Publications: 0, Preprints: 1, Total citations: 11

Preprints
"CellView: Interactive exploration of high dimensional single cell RNA-seq data"
DOI: 10.1101/123810, Citations: 11

Platform: R
Code: https://github.com/mohanbolisetty/CellView
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License: MIT
Categories: Interactive, Visualisation
Added: 2018-04-17, Updated: 2018-04-17

cellxgene

cellxgene is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas
Platform: Python/Javascript
Code: https://github.com/chanzuckerberg/cellxgene
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License: MIT
Categories: Interactive, Visualisation
Added: 2019-01-11, Updated: 2019-01-11

cellxgene_VIP

Enhanced plotting functions plugin for cellxgene

Publications: 0, Preprints: 2, Total citations: 24

Preprints
"Cellxgene VIP unleashes full power of interactive visualization and integrative analysis of scRNA-seq, spatial transcriptomics, and multiome data"
DOI: 10.1101/2020.08.28.270652, Citations: 24
"Cellxgene VIP unleashes full power of interactive visualization and integrative analysis of scRNA-seq, spatial transcriptomics, and multiome data"
DOI: 10.21203/rs.3.rs-1544196/v1, Citations: 0

Platform: Python
Code: https://github.com/interactivereport/cellxgene_VIP
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License: MIT
Categories: Interactive, Visualisation
Added: 2020-09-10, Updated: 2022-05-20

Cerebro

Cerebro, cell report browser, (currently available for macOS and Windows) which allows users to interactively visualize various parts of single cell transcriptomics data without requiring bioinformatic expertise.

Publications: 1, Preprints: 1, Total citations: 59

Publications
"Cerebro: interactive visualization of scRNA-seq data"
DOI: 10.1093/bioinformatics/btz877, Published: 2019-11-25, Citations: 54
Preprints
"Cerebro: Interactive visualization of scRNA-seq data"
DOI: 10.1101/631705, Citations: 5

Platform: C/C++/R/JavaScript
Code: https://github.com/romanhaa/Cerebro
starsN/A
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last commitUnknown
License: MIT
Categories: Gene Sets, Interactive, Visualisation
Added: 2019-11-06, Updated: 2019-11-06

CHETAH

CHETAH (CHaracterization of cEll Types Aided by Hierarchical clustering): a selective, hierarchical cell type identification method for single-cell RNA sequencing

Publications: 1, Preprints: 1, Total citations: 207

Publications
"CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing"
DOI: 10.1093/nar/gkz543, Published: 2019-06-21, Citations: 197
Preprints
"CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing"
DOI: 10.1101/558908, Citations: 10

Platform: R
Code: https://github.com/jdekanter/CHETAH
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License: AGPL-3.0
Categories: Classification, Interactive, Normalisation, Visualisation
Added: 2019-03-01, Updated: 2019-03-01

CIPR

Cluster Identity PRedictor (CIPR) provides a graphical user interface to quickly score gene expression profiles of unknown cell clusters against mouse or human references

Publications: 1, Preprints: 0, Total citations: 58

Publications
"CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments"
DOI: 10.1186/s12859-020-3538-2, Published: 2020-05-15, Citations: 58

Platform: R
Code: https://github.com/atakanekiz/CIPR-Package
starsN/A
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License: GPL-3.0
Categories: Classification, Interactive, Marker Genes, Visualisation
Added: 2020-05-22, Updated: 2020-05-22

Cirrocumulus

Cirrocumulus is an interactive visualization tool for large-scale single-cell genomics data
Platform: Python/JavaScript
Code: https://github.com/klarman-cell-observatory/cirrocumulus
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License: BSD-3-Clause
Categories: Interactive, Visualisation
Added: 2020-10-05, Updated: 2020-10-05

CiteFuse

CiteFuse is a streamlined package consisting of a suite of tools for pre-processing, modality integration, clustering, differential RNA and ADT expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualization of CITE-seq data

Publications: 1, Preprints: 1, Total citations: 76

Publications
"CiteFuse enables multi-modal analysis of CITE-seq data"
DOI: 10.1093/bioinformatics/btaa282, Published: 2020-04-30, Citations: 75
Preprints
"CiteFuse enables multi-modal analysis of CITE-seq data"
DOI: 10.1101/854299, Citations: 1

Platform: R
Code: https://github.com/SydneyBioX/CiteFuse
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last commitUnknown
License: GPL-3.0
Categories: Clustering, Differential Expression, Interactive, Quality Control, Visualisation
Added: 2019-12-01, Updated: 2021-06-11

CITEViz

CITEViz is a single-cell visualization platform with a custom module that replicates the interactive flow-cytometry gating workflow

Publications: 1, Preprints: 1, Total citations: 1

Publications
"CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny"
DOI: 10.1186/s12859-024-05762-1, Published: 2024-04-02, Citations: 0
Preprints
"CITE-Viz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq"
DOI: 10.1101/2022.05.15.491411, Citations: 1

Platform: R
Code: https://github.com/maxsonBraunLab/CITEViz
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License: MIT
Categories: Classification, Interactive, Visualisation
Added: 2024-04-12, Updated: 2024-04-12

Clustergrammer2

Clustergrammer2 is an interactive WebGL heatmap Jupyter widget that is built to help researchers interactively explore single cell data (e.g. scRNA-seq). Clustergrammer2 enables unbiased hierarchical clustering, integration of prior knowledge categories, and the generation of novel signatures.
Platform: Python
Code: https://github.com/ismms-himc/clustergrammer2
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License: MIT
Categories: Classification, Clustering, Gene Sets, Interactive, Visualisation
Added: 2019-11-06, Updated: 2021-06-28

Corvo

Corvo is a tool for the visualization of dimensionally reduced single-cell transcriptomics datasets in virtual reality

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"Corvo: Visualizing CellxGene Single-Cell Datasets in Virtual Reality"
arXiv: 2212.00519, Citations: 0

Platform: Kotlin/GLSL
Code: https://github.com/scenerygraphics/corvo-core
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Categories: Interactive, Visualisation
Added: 2022-12-09, Updated: 2022-12-09

E

ESCORT

Escort is a framework for evaluating a single-cell RNA-seq dataset’s suitability for trajectory inference and for quantifying trajectory properties influenced by analysis decisions

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference"
DOI: 10.1101/2023.12.18.572214, Citations: 0

Platform: R
Code: https://github.com/xiaorudong/Escort
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License: MIT
Categories: Clustering, Differential Expression, Dimensionality Reduction, Interactive, Ordering, Variable Genes
Added: 2024-01-05, Updated: 2024-01-05

F

FastProject

Here we present FastProject, a software package for two-dimensional visualization of single cell data, which utilizes a plethora of projection methods and provides a way to systematically investigate the biological relevance of these low dimensional representations by incorporating domain knowledge.

Publications: 1, Preprints: 0, Total citations: 58

Publications
"FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data"
DOI: 10.1186/s12859-016-1176-5, Published: 2016-08-23, Citations: 58

Platform: Python
Code: https://github.com/YosefLab/FastProject
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last commitUnknown
License: Custom
Categories: Dimensionality Reduction, Gene Sets, Interactive, Visualisation
Added: 2016-09-09, Updated: 2016-09-09

FEM

An algorithm which converts the gene expression matrix into a functional expression matrix

Publications: 1, Preprints: 0, Total citations: 2

Publications
"FEM: mining biological meaning from cell level in single-cell RNA sequencing data"
DOI: 10.7717/peerj.12570, Published: 2021-11-30, Citations: 2

Platform: Python
Code: https://github.com/qingyunpkdd/single_cell_fem
starsN/A
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last commitUnknown
Categories: Interactive, Quantification
Added: 2021-12-10, Updated: 2021-12-10

flotilla

Reproducible machine learning analysis of gene expression and alternative splicing data
Platform: Python
Code: https://github.com/yeolab/flotilla
starsN/A
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last commitUnknown
License: BSD-3-Clause
Categories: Clustering, Dimensionality Reduction, Gene Networks, Interactive, Quality Control
Added: 2016-09-08, Updated: 2021-06-28

FLOWMAPR

Graph-based visualizations of high-dimensional single-cell data across time

Publications: 1, Preprints: 0, Total citations: 19

Publications
"FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets"
DOI: 10.1038/s41596-019-0246-3, Published: 2020-01-13, Citations: 19

Platform: R
Code: https://github.com/zunderlab/FLOWMAP
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License: MIT
Categories: Interactive, Visualisation
Added: 2020-01-22, Updated: 2020-01-22

FRmatch

Cluster-to-cluster Mapping of Single Cell RNA Sequencing (scRNA-seq) Data Clusters by Friedman-Rafsky (FR) Test

Publications: 1, Preprints: 1, Total citations: 11

Publications
"FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test"
DOI: 10.1093/bib/bbaa339, Published: 2020-11-30, Citations: 9
Preprints
"FR-Match: A non-parametric multivariate statistical test for matching gene expression clusters from single cell RNA sequencing experiments"
DOI: 10.1101/2020.05.01.073445, Citations: 2

Platform: R
Code: https://github.com/JCVenterInstitute/FRmatch
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License: MIT
Categories: Classification, Interactive, Visualisation
Added: 2020-05-07, Updated: 2020-05-07

FUNKI

FUNKI is a multi-omic functional integration and analysis platform

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"FUNKI: Interactive functional footprint-based analysis of omics data"
arXiv: 2109.05796, Citations: 0

Platform: R
Code: https://github.com/saezlab/ShinyFUNKI
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License: AGPL-3.0
Categories: Gene Networks, Interactive, Visualisation
Added: 2021-09-24, Updated: 2021-09-24

G

GenePattern

Interactive notebook workflow for pre-processing data, identification of sub-populations of cells by clustering, and exploration of biomarkers.

Publications: 1, Preprints: 0, Total citations: 4

Publications
"An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data"
DOI: 10.12688/f1000research.15830.1, Published: 2018-08-16, Citations: 4

Platform: Python
Code: https://github.com/genepattern/single_cell_clustering_notebook
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last commitUnknown
License: BSD-3-Clause
Categories: Clustering, Dimensionality Reduction, Interactive, Marker Genes, Normalisation, Quality Control, Visualisation
Added: 2018-08-24, Updated: 2019-10-02

GiniClust

GiniClust is a clustering method implemented in Python and R for detecting rare cell-types from large-scale single-cell gene expression data.

Publications: 1, Preprints: 0, Total citations: 239

Publications
"GiniClust: detecting rare cell types from single-cell gene expression data with Gini index"
DOI: 10.1186/s13059-016-1010-4, Published: 2016-07-01, Citations: 239

Platform: R/Python
Code: https://github.com/lanjiangboston/GiniClust
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License: MIT
Categories: Clustering, Dimensionality Reduction, Interactive, Normalisation, Rare Cells
Added: 2016-09-09, Updated: 2016-09-09

GLUER

inteGrative anaLysis of mUlti-omics at single-cEll Resolution

Publications: 0, Preprints: 1, Total citations: 19

Preprints
"GLUER: integrative analysis of single-cell omics and imaging data by deep neural network"
DOI: 10.1101/2021.01.25.427845, Citations: 19

Platform: Python
Code: https://github.com/tanlabcode/GLUER
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License: MIT
Categories: Dimensionality Reduction, Integration, Interactive, Visualisation
Added: 2021-02-26, Updated: 2021-02-26

Granatum

This is a graphical single-cell RNA-seq (scRNA-seq) analysis pipeline for genomics scientists.

Publications: 1, Preprints: 1, Total citations: 62

Publications
"Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists"
DOI: 10.1186/s13073-017-0492-3, Published: 2017-12-05, Citations: 59
Preprints
"Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists"
DOI: 10.1101/110759, Citations: 3

Platform: Virtualbox
Code: https://gitlab.com/uhcclxgg/granatum
Categories: Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Networks, Gene Sets, Interactive, Normalisation, Ordering, Quality Control, Visualisation
Added: 2017-03-01, Updated: 2018-04-24

I

i2dash

The R package i2dash provides functionality to create customized, web-based dashboards for data presentation, exploration and sharing.

Publications: 1, Preprints: 1, Total citations: 2

Publications
"i2dash: Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics Data"
DOI: 10.1016/j.gpb.2021.01.007, Published: 2021-07, Citations: 1
Preprints
"i2dash: Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics-pipeline Results"
DOI: 10.1101/2020.07.06.189563, Citations: 1

Platform: R
Code: https://gitlab.gwdg.de/loosolab/software/i2dash
License: MIT
Categories: Interactive, Visualisation
Added: 2020-07-10, Updated: 2021-07-27

ICARUS

Welcome to ICARUS (Interactive single Cell RNA-seq Analysis with R shiny Using Seurat)

Publications: 2, Preprints: 1, Total citations: 36

Publications
"ICARUS, an interactive web server for single cell RNA-seq analysis"
DOI: 10.1093/nar/gkac322, Published: 2022-05-10, Citations: 31
"Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2.0"
DOI: 10.1093/nargab/lqad032, Published: 2022-06-01, Citations: 4
Preprints
"Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2.0"
DOI: 10.1101/2023.01.23.525100, Citations: 1

Platform: R
Code: https://github.com/Enjewl/ICARUS
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License: MIT
Categories: Cell Cycle, Classification, Differential Expression, Dimensionality Reduction, Gene Networks, Gene Sets, Imputation, Interactive, Marker Genes, Quality Control, Variants, Visualisation
Added: 2023-01-27, Updated: 2023-05-12

indeXplorer

indeXplorer is a web-based App written with shiny for the explorative analysis of index-sorted, single-cell transcriptomic data.

Publications: 1, Preprints: 0, Total citations: 5

Publications
"Demystifying blood stem cell fates"
DOI: 10.1038/ncb3494, Published: 2017-03-31, Citations: 5

Platform: R
Code: https://git.embl.de/velten/indeXplorer/
License: GPL-3.0
Categories: Interactive, Visualisation
Added: 2018-02-16, Updated: 2018-02-16

InterCellar

An R/Shiny app for interactive analysis and exploration of cell-cell communication based on single-cell transcriptomics data

Publications: 1, Preprints: 1, Total citations: 17

Publications
"InterCellar enables interactive analysis and exploration of cell−cell communication in single-cell transcriptomic data"
DOI: 10.1038/s42003-021-02986-2, Published: 2022-01-11, Citations: 16
Preprints
"Interactive analysis and exploration of cell-cell communication in single-cell transcriptomics with InterCellar"
DOI: 10.21203/rs.3.rs-525466/v1, Citations: 1

Platform: R
Code: https://github.com/martaint/InterCellar
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License: MIT
Categories: Gene Networks, Interactive, Visualisation
Added: 2021-05-21, Updated: 2022-01-22

iS-CellR

iS-CellR (Interactive platform for Single-cell RNAseq) is a web-based Shiny application designed to provide a comprehensive analysis of single-cell RNA sequencing data.

Publications: 1, Preprints: 0, Total citations: 20

Publications
"iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data"
DOI: 10.1093/bioinformatics/bty517, Published: 2018-07-04, Citations: 20

Platform: R
Code: https://github.com/immcore/iS-CellR
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last commitUnknown
License: GPL-3.0
Categories: Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Interactive, Normalisation, Quality Control, Variable Genes, Visualisation
Added: 2018-11-09, Updated: 2018-11-09

iscandar

Iscandar (Interactive Single Cell Data Analysis Report) is a set of python scripts and html/javascript files used to create interactive report for single cell rna-seq analysis.
Platform: Python
Code: https://github.com/jarny/iscandar
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last commitUnknown
License: MIT
Categories: Interactive, Visualisation
Added: 2017-11-20, Updated: 2017-11-20

iSEE

The SummarizedExplorer package aims to provide an interactive user interface for exploring data in SummarizedExperiment objects. Particular focus will be given to single-cell data in the SingleCellExperiment derived class.

Publications: 1, Preprints: 0, Total citations: 94

Publications
"iSEE: Interactive SummarizedExperiment Explorer"
DOI: 10.12688/f1000research.14966.1, Published: 2018-06-14, Citations: 94

Platform: R
Code: https://github.com/csoneson/iSEE
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License: MIT
Categories: Interactive, Visualisation
Added: 2018-01-19, Updated: 2018-06-19

K

kana

kana is a web application for single-cell RNA-seq data analysis that works directly in the browser

Publications: 1, Preprints: 1, Total citations: 4

Publications
"Powering single-cell analyses in the browser with WebAssembly"
DOI: 10.21105/joss.05603, Published: 2023-09-05, Citations: 1
Preprints
"Single-cell data analysis in the browser"
DOI: 10.1101/2022.03.02.482701, Citations: 3

Platform: JavaScript
Code: https://github.com/jkanche/kana
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License: MIT
Categories: Classification, Clustering, Dimensionality Reduction, Interactive, Marker Genes, Normalisation, Quality Control, Variable Genes, Visualisation
Added: 2022-03-11, Updated: 2024-01-05

L

langevitour

Interactive, animated 2D projections of high-D datasets

Publications: 1, Preprints: 1, Total citations: 1

Publications
"langevitour: Smooth Interactive Touring of High Dimensions, Demonstrated with scRNA-Seq Data"
DOI: 10.32614/RJ-2023-046, Published: 2023-11-01, Citations: 1
Preprints
"langevitour: smooth interactive touring of high dimensions, demonstrated with scRNA-Seq data"
DOI: 10.1101/2022.08.24.505207, Citations: 0

Platform: R/Python/Javascript
Code: https://github.com/pfh/langevitour
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License: MIT
Categories: Dimensionality Reduction, Interactive, Visualisation
Added: 2023-11-17, Updated: 2023-11-17

M

MAGIC

Markov Affinity-based Graph Imputation of Cells (MAGIC)

Publications: 1, Preprints: 1, Total citations: 1394

Publications
"Recovering Gene Interactions from Single-Cell Data Using Data Diffusion"
DOI: 10.1016/j.cell.2018.05.061, Published: 2018-07, Citations: 1333
Preprints
"MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data"
DOI: 10.1101/111591, Citations: 61

Platform: Python/R/MATLAB
Code: https://github.com/KrishnaswamyLab/MAGIC
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last commitUnknown
License: GPL-2.0
Categories: Dimensionality Reduction, Imputation, Interactive, Quality Control, Visualisation
Added: 2017-02-27, Updated: 2019-10-02

MCXpress

MCA is a dimensionality reduction technique that allows the representation of both individuals (cells) and the variables (genes) within the same Euclidean space, thus allowing the simultaneous identification of subpopulations of cells and their gene signatures.
Platform: R
Code: https://github.com/ARTbio/MCXpress
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last commitUnknown
License: MIT
Categories: Clustering, Dimensionality Reduction, Gene Filtering, Gene Sets, Interactive, Variable Genes
Added: 2018-03-15, Updated: 2021-06-28

O

OEFinder

Identify ordering effect genes in single cell RNA-seq data. OEFinder shiny impelemention depends on packages shiny, shinyFiles, gdata, and EBSeq.

Publications: 1, Preprints: 1, Total citations: 17

Publications
"OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data"
DOI: 10.1093/bioinformatics/btw004, Published: 2016-01-06, Citations: 16
Preprints
"OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data"
DOI: 10.1101/025437, Citations: 1

Platform: R
Code: https://github.com/lengning/OEFinder
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last commitUnknown
Categories: Interactive, Normalisation, Quality Control
Added: 2016-09-08, Updated: 2016-09-08

P

pagoda2

Single Cell Analysis and Differential Expression
Platform: R/C++
Code: https://github.com/hms-dbmi/pagoda2
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last commitUnknown
License: GPL-3.0
Categories: Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Sets, Interactive, Normalisation, Quality Control, Visualisation
Added: 2018-11-09, Updated: 2021-01-29

PIVOT

PIVOT facilitates fast and interactive RNA-Seq data analysis and visualization.

Publications: 1, Preprints: 1, Total citations: 37

Publications
"PIVOT: platform for interactive analysis and visualization of transcriptomics data"
DOI: 10.1186/s12859-017-1994-0, Published: 2018-01-05, Citations: 36
Preprints
"PIVOT: Platform for Interactive Analysis and Visualization of Transcriptomics Data"
DOI: 10.1101/053348, Citations: 1

Platform: R
Code: https://github.com/qinzhu/PIVOT
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last commitUnknown
License: Custom
Categories: Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Networks, Gene Sets, Interactive, Normalisation, Ordering, Quality Control, Visualisation
Added: 2017-07-16, Updated: 2018-03-14

PySCUBA

PySCUBA stands for "Python for Single-cell Clustering Using Bifurcation Analysis"

Publications: 1, Preprints: 0, Total citations: 251

Publications
"Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape"
DOI: 10.1073/pnas.1408993111, Published: 2014-12-15, Citations: 251

Platform: Python
Code: https://github.com/GGiecold/PySCUBA
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last commitUnknown
License: MIT
Categories: Clustering, Interactive, Ordering, Visualisation
Added: 2021-08-11, Updated: 2021-08-11

S

sake

Single-cell RNA-Seq Analysis and Klustering Evaluation. The aim of sake is to provide a user-friendly tool for easy analysis of NGS Single-Cell transcriptomic data.
Platform: R
Code: https://github.com/naikai/sake
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License: GPL-2.0-or-later
Categories: Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Networks, Gene Sets, Interactive, Normalisation, Visualisation
Added: 2016-10-10, Updated: 2016-10-10

SAM

The self-assembling manifold (SAM) algorithm, an iterative soft feature selection strategy to quantify gene relevance and improve dimensionality reduction.

Publications: 1, Preprints: 1, Total citations: 66

Publications
"Self-assembling manifolds in single-cell RNA sequencing data"
DOI: 10.7554/eLife.48994, Published: 2019-09-16, Citations: 63
Preprints
"Self-assembling Manifolds in Single-cell RNA Sequencing Data"
DOI: 10.1101/364166, Citations: 3

Platform: Python
Code: https://github.com/atarashansky/self-assembling-manifold
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last commitUnknown
License: MIT
Categories: Clustering, Dimensionality Reduction, Gene Filtering, Interactive, Marker Genes, Normalisation, Visualisation
Added: 2019-11-03, Updated: 2021-06-28

SC3

SC3 is an interactive tool for the unsupervised clustering of cells from single cell RNA-Seq experiments.

Publications: 1, Preprints: 1, Total citations: 1274

Publications
"SC3: consensus clustering of single-cell RNA-seq data"
DOI: 10.1038/nmeth.4236, Published: 2017-03-27, Citations: 1236
Preprints
"SC3 - consensus clustering of single-cell RNA-Seq data"
DOI: 10.1101/036558, Citations: 38

Platform: R
Code: https://github.com/hemberg-lab/sc3
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last commitUnknown
License: GPL-3.0
Categories: Clustering, Interactive
Added: 2016-09-08, Updated: 2018-03-14

SCALA

A web application for multimodal analysis of single cell next generation sequencing data

Publications: 1, Preprints: 1, Total citations: 3

Publications
"SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data"
DOI: 10.1016/j.csbj.2023.10.032, Published: 2023, Citations: 2
Preprints
"SCALA: A web application for multimodal analysis of single cell next generation sequencing data"
DOI: 10.1101/2022.11.24.517826, Citations: 1

Platform: R/JavaScript
Code: https://github.com/PavlopoulosLab/SCALA
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last commitUnknown
License: GPL-3.0
Categories: Cell Cycle, Classification, Clustering, Differential Expression, Dimensionality Reduction, Expression Patterns, Gene Filtering, Gene Networks, Integration, Interactive, Marker Genes, Normalisation, Ordering, Quality Control, Variable Genes, Visualisation
Added: 2023-11-17, Updated: 2023-11-17

scASK

scASK is a novel and robust ensemble framework that is especially suited for cell type classification based on scRNA-seq data

Publications: 2, Preprints: 1, Total citations: 2

Publications
"scASK: A Novel Ensemble Framework for Classifying Cell Types Based on Single-cell RNA-seq Data"
DOI: 10.1109/jbhi.2021.3050963, Published: 2021, Citations: 1
"scASK: A Novel Ensemble Framework for Classifying Cell Types Based on Single-cell RNA-seq Data"
DOI: 10.1109/JBHI.2021.3050963, Published: 2021, Citations: 1
Preprints
"scASK: A novel ensemble framework for classifying cell types based on single-cell RNA-seq data"
DOI: 10.1101/2020.06.07.138271, Citations: 0

Platform: MATLAB
Code: https://github.com/liubo2358/scASKcmd
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last commitUnknown
Categories: Classification, Dimensionality Reduction, Interactive
Added: 2020-06-16, Updated: 2021-01-22

scClustViz

An interactive R Shiny tool for visualizing single-cell RNAseq clustering results from the Seurat R package or any other analysis pipeline.

Publications: 1, Preprints: 0, Total citations: 28

Publications
"scClustViz – Single-cell RNAseq cluster assessment and visualization"
DOI: 10.12688/f1000research.16198.1, Published: 2018-09-21, Citations: 28

Platform: R
Code: https://github.com/BaderLab/scClustViz
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License: MIT
Categories: Interactive, Visualisation
Added: 2018-07-27, Updated: 2018-10-03

scdiff

SCDIFF is a python package designed to analyze the cell differentiation process using time-series single cell RNA-seq data.

Publications: 1, Preprints: 0, Total citations: 43

Publications
"Reconstructing differentiation networks and their regulation from time series single-cell expression data"
DOI: 10.1101/gr.225979.117, Published: 2018-01-09, Citations: 43

Platform: Python
Code: https://github.com/phoenixding/scdiff
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last commitUnknown
License: MIT
Categories: Gene Networks, Interactive, Ordering, Visualisation
Added: 2018-01-18, Updated: 2018-03-07

SCell

SCell is an integrated software tool for quality filtering, normalization, feature selection, iterative dimensionality reduction, clustering and the estimation of gene-expression gradients from large ensembles of single-cell RNA-seq datasets. SCell is open source, and implemented with an intuitive graphical interface.

Publications: 1, Preprints: 0, Total citations: 43

Publications
"SCell: integrated analysis of single-cell RNA-seq data"
DOI: 10.1093/bioinformatics/btw201, Published: 2016-04-19, Citations: 43

Platform: MATLAB
Code: https://github.com/diazlab/SCell
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last commitUnknown
License: GPL-1.0
Categories: Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Interactive, Normalisation, Ordering, Quality Control, Visualisation
Added: 2016-09-08, Updated: 2016-09-08

SCelVis

SCelVis: Easy Single-Cell Visualization

Publications: 1, Preprints: 1, Total citations: 8

Publications
"SCelVis: exploratory single cell data analysis on the desktop and in the cloud"
DOI: 10.7717/peerj.8607, Published: 2020-02-19, Citations: 7
Preprints
"SCelVis: Powerful explorative single cell data analysis on the desktop and in the cloud"
DOI: 10.1101/713008, Citations: 1

Platform: Python
Code: https://github.com/bihealth/scelvis
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last commitUnknown
License: MIT
Categories: Interactive, Visualisation
Added: 2019-08-05, Updated: 2020-03-03

scfind

scfind - Fast searches of large collections of single cell data

Publications: 1, Preprints: 1, Total citations: 12

Publications
"Fast searches of large collections of single-cell data using scfind"
DOI: 10.1038/s41592-021-01076-9, Published: 2021-03-01, Citations: 10
Preprints
"Fast searches of large collections of single cell data using scfind"
DOI: 10.1101/788596, Citations: 2

Platform: R/C++
Code: https://github.com/hemberg-lab/scfind
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last commitUnknown
License: GPL-3.0
Categories: Classification, Interactive, Marker Genes
Added: 2019-10-09, Updated: 2021-06-28

scGESTALT

This Docker image processes GESTALT barcode sequencing data. Reads are merged by UMI, aligned to the reference file, and aggregated into plots describing the overall editing, as well as trees describing the relative lineage relationships within your data.

Publications: 1, Preprints: 1, Total citations: 73

Publications
"Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR–Cas9 barcodes by scGESTALT"
DOI: 10.1038/s41596-018-0058-x, Published: 2018-10-23, Citations: 64
Preprints
"Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain by scGESTALT"
DOI: 10.1101/205534, Citations: 9

Platform: Scala
Code: https://github.com/aaronmck/SC_GESTALT
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last commitUnknown
Categories: Alignment, Interactive, Ordering, UMIs, Visualisation
Added: 2018-10-29, Updated: 2018-10-29

SCHNAPPs

Shiny app for the exploration and analysis of single cell RNAseq data as it comes from 10X or MARSseq technologies.

Publications: 1, Preprints: 1, Total citations: 12

Publications
"SCHNAPPs - Single Cell sHiNy APPlication(s)"
DOI: 10.1016/j.jim.2021.113176, Published: 2021-12, Citations: 11
Preprints
"SCHNAPPs - Single Cell sHiNy APPlication(s)"
DOI: 10.1101/2020.06.07.127274, Citations: 1

Platform: R
Code: https://github.com/C3BI-pasteur-fr/UTechSCB-SCHNAPPs
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last commitUnknown
License: GPL-3.0
Categories: Differential Expression, Dimensionality Reduction, Interactive, Quality Control, Visualisation
Added: 2019-05-17, Updated: 2021-11-27

scicast

Single Cell Iterative Clustering and Significance Testing
Platform: Python
Code: https://github.com/iandriver/SCICAST
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last commitUnknown
License: MIT
Categories: Clustering, Dimensionality Reduction, Interactive, Marker Genes, Normalisation, Visualisation
Added: 2018-11-13, Updated: 2018-11-13

scIVA

scIVA - Single Cell Interactive Visualisation and Analysis
Platform: R
Code: https://github.com/IMB-Computational-Genomics-Lab/scIVA
starsN/A
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last commitUnknown
Categories: Gene Sets, Interactive, Marker Genes, Quality Control, Visualisation
Added: 2018-12-13, Updated: 2018-12-13

Sciviewer

This is an interactive viewer for 2D embeddings such as UMAP or tSNE of high dimensional single-cell RNA-seq data that is run directly out of the Jupyter Notebook environment

Publications: 1, Preprints: 1, Total citations: 2

Publications
"Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment"
DOI: 10.1093/bioinformatics/btab689, Published: 2021-10-02, Citations: 2
Preprints
"Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment"
DOI: 10.1101/2021.08.12.455997, Citations: 0

Platform: Python
Code: https://github.com/colabobio/sciviewer
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last commitUnknown
License: MIT
Categories: Interactive, Visualisation
Added: 2021-08-27, Updated: 2021-10-18

scNetViz

A Cytoscape app to aid biological interpretation of cell clusters in scRNA-seq data using network analysis

Publications: 1, Preprints: 0, Total citations: 0

Publications
"scNetViz: from single cells to networks using Cytoscape"
DOI: 10.12688/f1000research.52460.1, Published: 2021-06-07, Citations: 0

Platform: Java
Code: https://github.com/RBVI/scNetViz
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last commitUnknown
License: Apache-2.0
Categories: Gene Networks, Interactive, Visualisation
Added: 2021-06-18, Updated: 2021-06-18

SCNS

The Single Cell Network Synthesis tool (SCNS) is a tool for the reconstruction and analysis of executable models from single-cell gene expression data.

Publications: 1, Preprints: 0, Total citations: 68

Publications
"SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data"
DOI: 10.1186/s12918-018-0581-y, Published: 2018-05-25, Citations: 68

Platform: Javascript/F#
Code: https://github.com/swoodhouse/SCNS-GUI
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Gene Networks, Interactive, Ordering, Visualisation
Added: 2018-06-01, Updated: 2018-06-01

scone

SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell RNA-seq data quality control (QC) and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.

Publications: 1, Preprints: 1, Total citations: 135

Publications
"Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq"
DOI: 10.1016/j.cels.2019.03.010, Published: 2019-04, Citations: 119
Preprints
"Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-seq"
DOI: 10.1101/235382, Citations: 16

Platform: R
Code: https://github.com/YosefLab/scone
starsN/A
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last commitUnknown
License: Artistic-2.0
Categories: Gene Filtering, Imputation, Interactive, Normalisation, Quality Control, Visualisation
Added: 2016-09-08, Updated: 2021-01-08

SCope

SCope: Visualization of large-scale and high dimensional single cell data

Publications: 1, Preprints: 1, Total citations: 698

Publications
"A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain"
DOI: 10.1016/j.cell.2018.05.057, Published: 2018-08, Citations: 693
Preprints
"A single-cell catalogue of regulatory states in the ageing Drosophila brain"
DOI: 10.1101/237420, Citations: 5

Platform: Python
Code: https://github.com/aertslab/SCope
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last commitUnknown
License: GPL-3.0
Categories: Clustering, Gene Sets, Interactive, Visualisation
Added: 2018-06-15, Updated: 2018-06-15

scopeplus

Scope+ is a modern, scalable and generalized single-cell atlas portal archictecture

Publications: 0, Preprints: 1, Total citations: 1

Preprints
"Scope+: An open source generalizable architecture for single-cell atlases at sample and cell levels"
DOI: 10.1101/2022.12.03.518997, Citations: 1

Platform: Python
Code: https://github.com/hiyin/scopeplus
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last commitUnknown
License: MIT
Categories: Interactive, Visualisation
Added: 2023-11-03, Updated: 2023-11-03

SCPattern

A statistical approach to identify and classify expression changes in single cell RNA-seq experiments with ordered conditions.

Publications: 0, Preprints: 1, Total citations: 1

Preprints
"SCPattern: A statistical approach to identify and classify expression changes in single cell RNA-seq experiments with ordered conditions"
DOI: 10.1101/046110, Citations: 1

Platform: R
Code: https://github.com/lengning/SCPattern
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last commitUnknown
License: Apache-2.0
Categories: Differential Expression, Expression Patterns, Interactive
Added: 2016-09-09, Updated: 2016-09-09

scPhere

ScPhere resolves cell crowding, corrects multiple, complex batch factors, facilitates interactive visualization of large datasets, and gracefully uncovers pseudotemporal trajectories.

Publications: 1, Preprints: 1, Total citations: 78

Publications
"Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces"
DOI: 10.1038/s41467-021-22851-4, Published: 2021-05-05, Citations: 66
Preprints
"Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces"
DOI: 10.1101/853457, Citations: 12

Platform: Python
Code: https://github.com/klarman-cell-observatory/scPhere
starsN/A
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last commitUnknown
License: BSD-3-Clause
Categories: Dimensionality Reduction, Interactive, Ordering, Visualisation
Added: 2019-12-01, Updated: 2019-12-01

scPlot

Single cell interactive plotting tools

Publications: 1, Preprints: 1, Total citations: 182

Publications
"Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq"
DOI: 10.1038/s41592-020-0905-x, Published: 2020-07-27, Citations: 174
Preprints
"Cumulus: a cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq"
DOI: 10.1101/823682, Citations: 8

Platform: Python
Code: https://github.com/klarman-cell-observatory/scPlot
starsN/A
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last commitUnknown
License: BSD-3-Clause
Categories: Interactive, Visualisation
Added: 2019-11-03, Updated: 2020-08-06

scPower

scPower is a R package for design and power analysis of cell type specific interindividual DE and eQTL studies using single cell RNA-seq

Publications: 1, Preprints: 1, Total citations: 62

Publications
"scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies"
DOI: 10.1038/s41467-021-26779-7, Published: 2021-11-16, Citations: 50
Preprints
"Design and power analysis for multi-sample single cell genomics experiments"
DOI: 10.1101/2020.04.01.019851, Citations: 12

Platform: R
Code: https://github.com/heiniglab/scPower
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last commitUnknown
License: GPL-3.0
Categories: Interactive, Simulation
Added: 2020-04-13, Updated: 2021-11-20

scQCEA

scQCEA (acronym of the single-cell RNA sequencing Quality Control and Enrichment Analysis) is an R package for annotation and quality control report of scRNA-Seq profiles

Publications: 1, Preprints: 0, Total citations: 2

Publications
"scQCEA: a framework for annotation and quality control report of single-cell RNA-sequencing data"
DOI: 10.1186/s12864-023-09447-6, Published: 2023-07-06, Citations: 2

Platform: R
Code: https://github.com/isarnassiri/scQCEA
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last commitUnknown
License: GPL-2.0
Categories: Classification, Interactive, Quality Control
Added: 2023-07-14, Updated: 2023-07-14

scran

This package implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, pool-based norms to estimate size factors, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.

Publications: 2, Preprints: 1, Total citations: 2823

Publications
"Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors"
DOI: 10.1038/nbt.4091, Published: 2018-04-02, Citations: 1877
"Pooling across cells to normalize single-cell RNA sequencing data with many zero counts"
DOI: 10.1186/s13059-016-0947-7, Published: 2016-04-27, Citations: 928
Preprints
"Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours"
DOI: 10.1101/165118, Citations: 18

Platform: R
Code: https://github.com/MarioniLab/scran
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last commitUnknown
License: GPL-3.0
Categories: Cell Cycle, Integration, Interactive, Normalisation, Variable Genes, Visualisation
Added: 2016-09-08, Updated: 2018-04-02

scRNAseqApp

scRNAseqApp is a Shiny app package that allows users to visualize single cell data interactively
Platform: R/JavaScript/CSS
Code: https://github.com/jianhong/scRNAseqApp
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last commitUnknown
License: GPL-3.0
Categories: Interactive, Visualisation
Added: 2023-05-05, Updated: 2023-05-05

scSeqR

scSeqR (Single Cell Sequencing R package) is an interactive R package to works with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq and CITE-seq).
Platform: R
Code: https://github.com/rezakj/scSeqR
starsN/A
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last commitUnknown
License: GPL-2.0
Categories: Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Sets, Integration, Interactive, Marker Genes, Normalisation, Quality Control, Visualisation
Added: 2018-11-09, Updated: 2018-11-09

scSO

scSO is a new algorithm for scRNA-seq data clustering based on Sparse Optimization and low-rank matrix factorization

Publications: 1, Preprints: 0, Total citations: 1

Publications
"Single-cell data clustering based on sparse optimization and low-rank matrix factorization"
DOI: 10.1093/g3journal/jkab098, Published: 2021-03-31, Citations: 1

Platform: MATLAB/Python/C++/Fortran
Code: https://github.com/QuKunLab/scSO
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last commitUnknown
License: BSD-2-Clause
Categories: Clustering, Dimensionality Reduction, Interactive
Added: 2021-04-12, Updated: 2021-04-12

scSTEM

Single cell STEM (scSTEM) is a shiny app based R package for visualizing and clustering genes in pseudotime ordered single cell RNA-seq data

Publications: 1, Preprints: 0, Total citations: 7

Publications
"scSTEM: clustering pseudotime ordered single-cell data"
DOI: 10.1186/s13059-022-02716-9, Published: 2022-07-07, Citations: 7

Platform: R
Code: https://github.com/alexQiSong/scSTEM
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last commitUnknown
License: GPL-3.0-or-later
Categories: Clustering, Expression Patterns, Interactive, Ordering, Visualisation
Added: 2022-08-12, Updated: 2022-08-12

scSVA

An R package for interactive two- and three-dimensional visualization and exploration of massive single-cell omics data.

Publications: 0, Preprints: 1, Total citations: 15

Preprints
"scSVA: an interactive tool for big data visualization and exploration in single-cell omics"
DOI: 10.1101/512582, Citations: 15

Platform: R
Code: https://github.com/klarman-cell-observatory/scSVA
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last commitUnknown
License: GPL-3.0
Categories: Dimensionality Reduction, Interactive, Visualisation
Added: 2019-01-14, Updated: 2019-01-14

scTreeViz

This package provides methods to interactively explore and visualize datasets with hierarchies. eg. single cells datasets with hierarchy over cells at different resolutions
Platform: R
Code: https://github.com/HCBravoLab/scTreeViz
starsN/A
forksN/A
last commitUnknown
License: Artistic-2.0
Categories: Interactive, Visualisation
Added: 2021-10-29, Updated: 2021-10-29

scViewer

A single-cell data viewer shiny application

Publications: 1, Preprints: 0, Total citations: 3

Publications
"scViewer: An Interactive Single-Cell Gene Expression Visualization Tool"
DOI: 10.3390/cells12111489, Published: 2023-05-27, Citations: 3

Platform: R
Code: https://github.com/arpatil01/scViewer
starsN/A
forksN/A
last commitUnknown
Categories: Interactive, Visualisation
Added: 2023-09-08, Updated: 2023-09-08

scVirtualCyto

Single-Cell Virtual Cytometer is an open source software for straightforward visualization and exploration of multimodal single cell datasets as in flow cytometry.

Publications: 1, Preprints: 1, Total citations: 13

Publications
"Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets"
DOI: 10.1093/nargab/lqaa025, Published: 2020-04-20, Citations: 13
Preprints
"Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets"
DOI: 10.1101/843946, Citations: 0

Platform: Javascript
Code: https://github.com/FredPont/single-cell-virtual-cytometer
starsN/A
forksN/A
last commitUnknown
License: AGPL-3.0
Categories: Interactive, Visualisation
Added: 2019-11-21, Updated: 2020-05-14

scWizard

scWizard is a tool with graphical user interface (GUI) for cancer single cell RNA-seq data analysis

Publications: 1, Preprints: 0, Total citations: 0

Publications
"scWizard: a web-based automated tool for classifying and annotating single cells and downstream analysis of single-cell RNA-seq data in cancers"
DOI: 10.1016/j.csbj.2022.08.028, Published: 2022-08, Citations: 0

Platform: R/Python
Code: https://github.com/Dulab2020/scWizard
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0-or-later
Categories: Classification, Clustering, Gene Networks, Gene Sets, Integration, Interactive, Ordering, Quality Control, Variants, Visualisation
Added: 2022-09-02, Updated: 2022-09-02

scX

scX is an R package that enables interactive visualization and analysis of single-cell experiment data

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"scX: A user-friendly tool for scRNA-seq exploration"
arXiv: 2311.00012, Citations: 0

Platform: R
Code: https://github.com/chernolabs/scX
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Differential Expression, Interactive, Marker Genes, Visualisation
Added: 2023-11-10, Updated: 2023-11-10

SEPA

SEPA provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment analysis to analysis the functional roles of genes with same or similar patterns.
Platform: R
Code: https://github.com/zji90/SEPA
starsN/A
forksN/A
last commitUnknown
License: GPL-2.0-or-later
Categories: Expression Patterns, Gene Sets, Interactive
Added: 2016-09-08, Updated: 2016-09-08

SEQUIN

SEQUIN is an R/Shiny application for analysis and visualization of bulk and single-cell RNA-seq data

Publications: 1, Preprints: 1, Total citations: 1

Publications
"SEQUIN: Rapid and Reproducible Analysis of RNA-Seq Data in R/Shiny"
DOI: 10.2139/ssrn.4193117, Published: 2022, Citations: 0
Preprints
"SEQUIN: rapid and reproducible analysis of RNA-seq data in R/Shiny"
DOI: 10.1101/2022.02.23.481646, Citations: 1

Platform: R
Code: https://github.com/ncats/public_sequin
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Clustering, Gene Sets, Interactive, Quality Control, Visualisation
Added: 2022-03-04, Updated: 2023-01-04

SeuratV3Wizard

R Shiny interface for Seurat v3 single-cell analysis library
Platform: R
Code: https://github.com/nasqar/seuratv3wizard
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Clustering, Dimensionality Reduction, Interactive, Marker Genes, Normalisation, Quality Control, Variable Genes
Added: 2019-03-01, Updated: 2019-03-01

SeuratWizard

R Shiny interface for Seurat single-cell analysis library
Platform: R
Code: https://github.com/nasqar/SeuratWizard
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Clustering, Dimensionality Reduction, Interactive, Marker Genes, Normalisation, Quality Control, Variable Genes
Added: 2019-01-18, Updated: 2021-06-28

ShinyCell

ShinyCell is a R package that allows users to create interactive Shiny-based web applications to visualise single-cell data

Publications: 1, Preprints: 1, Total citations: 144

Publications
"ShinyCell: simple and sharable visualization of single-cell gene expression data"
DOI: 10.1093/bioinformatics/btab209, Published: 2021-03-28, Citations: 139
Preprints
"ShinyCell: Simple and sharable visualisation of single-cell gene expression data"
DOI: 10.1101/2020.10.25.354100, Citations: 5

Platform: R
Code: https://github.com/SGDDNB/ShinyCell
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Interactive, Visualisation
Added: 2020-11-08, Updated: 2020-11-08

ShinyMultiome-UiO

An interactive open-source framework utilizing Seurat Objects for visualizing single-cell Multiomes

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"ShinyMultiome.UiO: An interactive open-source framework utilizing Seurat Objects for visualizing single-cell Multiomes"
DOI: 10.1101/2023.06.20.545756, Citations: 0

Platform: R
Code: https://github.com/EskelandLab/ShinyMultiomeUiO
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Interactive, Visualisation
Added: 2023-07-14, Updated: 2023-07-14

SiCR

A web application specialized for single cell repertoire analysis

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"SiCR: Web application for single-cell repertoire analysis and immune profiling"
DOI: 10.1101/2023.08.03.551897, Citations: 0

Platform: R
Categories: Immune, Interactive
Added: 2023-08-11, Updated: 2024-10-29

SigHotSpotter

A computational tool to predict hotspots of signaling pathways responsible for the stable maintenance of cell subpopulation phenotypes, by integrating signaling and transcriptional networks.

Publications: 1, Preprints: 0, Total citations: 12

Publications
"SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies"
DOI: 10.1093/bioinformatics/btz827, Published: 2019-11-07, Citations: 12

Platform: R
Code: https://gitlab.com/srikanth.ravichandran/sighotspotter
License: AGPL-3.0
Categories: Gene Networks, Gene Sets, Interactive, Visualisation
Added: 2019-11-15, Updated: 2019-11-15

SinCHet

a MATLAB GUI toolbox for Single Cell Heterogeneity analysis in cancer

Publications: 1, Preprints: 0, Total citations: 12

Publications
"SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer"
DOI: 10.1093/bioinformatics/btx297, Published: 2017-05-04, Citations: 12

Platform: MATLAB
Code: http://labpages2.moffitt.org/chen/software
Categories: Clustering, Interactive, Visualisation
Added: 2017-11-20, Updated: 2017-11-20

SingleCellExplorer

Single Cell Explorer is a Python-based web server application for computational and experimental scientists to iteratively and collaboratively annotate cell expression phenotypes within a user-friendly and visually appealing platform.

Publications: 1, Preprints: 0, Total citations: 23

Publications
"Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data"
DOI: 10.1186/s12864-019-6053-y, Published: 2019-08-27, Citations: 23

Platform: Python
Code: https://github.com/d-feng/scExplorer
starsN/A
forksN/A
last commitUnknown
License: LGPL-3.0
Categories: Interactive, Visualisation
Added: 2019-09-02, Updated: 2019-09-02

singleCellTK

Interactive Analysis of Single Cell RNA-Seq Data

Publications: 2, Preprints: 3, Total citations: 46

Publications
"Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data"
DOI: 10.1038/s41467-022-29212-9, Published: 2022-03-30, Citations: 38
"Interactive Analysis of Single-Cell Data Using Flexible Workflows With SCTK2.0"
DOI: 10.2139/ssrn.4174578, Published: 2022, Citations: 0
Preprints
"Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data"
DOI: 10.1101/2020.11.16.385328, Citations: 2
"Interactive analysis of single-cell data using flexible workflows with SCTK2.0"
DOI: 10.1101/2022.07.13.499900, Citations: 0
"Interactive single cell RNA-Seq analysis with the Single Cell Toolkit (SCTK)"
DOI: 10.1101/329755, Citations: 6

Platform: R
Code: https://github.com/compbiomed/singleCellTK
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Alignment, Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Sets, Interactive, Marker Genes, Normalisation, Quality Control, Quantification, Visualisation
Added: 2018-05-13, Updated: 2022-08-12

SinglePointRNA

SinglePoint RNA is a shiny-based R application that provides a graphic interface for different publicly available tools to analyze single cell RNA-seq data

Publications: 0, Preprints: 1, Total citations: 0

Preprints
"SinglePointRNA, an user-friendly application implementing single cell RNA-seq analysis software"
arXiv: 2305.00008, Citations: 0

Platform: R
Code: https://github.com/ScienceParkMadrid/SinglePointRNA
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Clustering, Differential Expression, Integration, Interactive, Quality Control, Visualisation
Added: 2023-05-28, Updated: 2023-05-28

SPEEDI

Single-cell Pipeline for End to End Data Integration (SPEEDI) is a fully automated, end-to-end pipeline that facilitates single cell data analysis and improves robustness and reproducibility

Publications: 0, Preprints: 1, Total citations: 1

Preprints
"Automated single-cell omics end-to-end framework with data-driven batch inference"
DOI: 10.1101/2023.11.01.564815, Citations: 1

Platform: R
Code: https://github.com/FunctionLab/SPEEDI
starsN/A
forksN/A
last commitUnknown
Categories: Classification, Clustering, Differential Expression, Dimensionality Reduction, Integration, Interactive, Quality Control, Visualisation
Added: 2023-11-10, Updated: 2023-11-10

SPRING

SPRING is a collection of pre-processing scripts and a web browser-based tool for visualizing and interacting with high dimensional data.

Publications: 1, Preprints: 1, Total citations: 271

Publications
"SPRING: a kinetic interface for visualizing high dimensional single-cell expression data"
DOI: 10.1093/bioinformatics/btx792, Published: 2017-12-07, Citations: 259
Preprints
"SPRING: a kinetic interface for visualizing high dimensional single-cell expression data"
DOI: 10.1101/090332, Citations: 12

Platform: Python/MATLAB/Javascript
Code: https://github.com/AllonKleinLab/SPRING
starsN/A
forksN/A
last commitUnknown
Categories: Dimensionality Reduction, Interactive, Visualisation
Added: 2016-12-05, Updated: 2016-12-05

starmapVis

StarmapVis enables interactive web-based visualisation for various single cell or spatial omic data

Publications: 1, Preprints: 0, Total citations: 1

Publications
"StarmapVis: An interactive and narrative visualisation tool for single-cell and spatial data"
DOI: 10.1016/j.csbj.2023.02.023, Published: 2023, Citations: 1

Platform: JavaScript
Code: https://github.com/holab-hku/starmapVis
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Interactive, Visualisation
Added: 2023-02-24, Updated: 2023-02-24

STREAM

STREAM is an interactive computational pipeline for reconstructing complex cellular developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data.

Publications: 1, Preprints: 1, Total citations: 206

Publications
"Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM"
DOI: 10.1038/s41467-019-09670-4, Published: 2019-04-23, Citations: 202
Preprints
"STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data"
DOI: 10.1101/302554, Citations: 4

Platform: Python/Docker
Code: https://github.com/pinellolab/stream
starsN/A
forksN/A
last commitUnknown
License: AGPL-3.0
Categories: Expression Patterns, Interactive, Normalisation, Ordering, Visualisation
Added: 2018-04-24, Updated: 2019-05-07

T

TASIC

TASIC uses a Hidden Markov Model (HMM) based on a probabilistic Kalman Filter approach to combine time and expression information for determining the branching process associated with time series single cell studies.

Publications: 1, Preprints: 0, Total citations: 32

Publications
"TASIC: determining branching models from time series single cell data"
DOI: 10.1093/bioinformatics/btx173, Published: 2017-04-04, Citations: 32

Platform: MATLAB
Code: https://www.andrew.cmu.edu/user/sabrinar/TASIC/TASIC.htm
Categories: Interactive, Ordering
Added: 2017-04-27, Updated: 2017-04-27

TooManyCellsInteractive

too-many-cells-interactive is an interactive visualization tool allowing users to explore cell cluster trees generated by too-many-cells

Publications: 0, Preprints: 1, Total citations: 3

Preprints
"TooManyCellsInteractive: a visualization tool for dynamic exploration of single-cell data"
DOI: 10.1101/2023.06.16.544954, Citations: 3

Platform: TypeScript
Code: https://github.com/schwartzlab-methods/too-many-cells-interactive
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Interactive, Visualisation
Added: 2023-07-07, Updated: 2023-07-07

TSCAN

Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.

Publications: 1, Preprints: 0, Total citations: 529

Publications
"TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis"
DOI: 10.1093/nar/gkw430, Published: 2016-05-13, Citations: 529

Platform: R
Code: https://github.com/zji90/TSCAN
starsN/A
forksN/A
last commitUnknown
License: GPL-2.0-or-later
Categories: Clustering, Interactive, Marker Genes, Ordering, Visualisation
Added: 2016-09-09, Updated: 2016-09-09

U

UNCURL

UNCURL is an unified framework for unsupervised / semi-supervised learning using Single Cell RNA-Seq data.

Publications: 1, Preprints: 2, Total citations: 25

Publications
"Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge"
DOI: 10.1093/bioinformatics/bty293, Published: 2018-06-27, Citations: 23
Preprints
"Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge"
DOI: 10.1101/142398, Citations: 0
"UNCURL-App: Interactive Database-Driven Analysis of Single Cell RNA Sequencing Data"
DOI: 10.1101/2020.04.15.043737, Citations: 2

Platform: Python
Code: https://github.com/yjzhang/uncurl_python
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Clustering, Dimensionality Reduction, Interactive, Ordering, Visualisation
Added: 2017-06-26, Updated: 2021-06-28

uSORT

This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization.
Platform: R
Code: https://github.com/JinmiaoChenLab/uSORT
starsN/A
forksN/A
last commitUnknown
License: Artistic-2.0
Categories: Differential Expression, Gene Filtering, Interactive, Ordering, Quality Control, Variable Genes
Added: 2018-08-31, Updated: 2018-08-31

V

VisCello

Viscello for Visualization of Single Cell Data

Publications: 1, Preprints: 1, Total citations: 440

Publications
"A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution"
DOI: 10.1126/science.aax1971, Published: 2019-09-05, Citations: 423
Preprints
"A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution"
DOI: 10.1101/565549, Citations: 17

Platform: R
Code: https://github.com/tanlabcode/VisCello
starsN/A
forksN/A
last commitUnknown
License: GPL-2.0
Categories: Dimensionality Reduction, Interactive, Visualisation
Added: 2021-02-26, Updated: 2021-02-26

VISION

VISION aids in the interpretation of single-cell RNA-seq (scRNA-seq) data by selecting for gene signatures which describe coordinated variation between cells

Publications: 2, Preprints: 2, Total citations: 215

Publications
"Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision"
DOI: 10.1016/j.crmeth.2022.100200, Published: 2022-04, Citations: 8
"Functional interpretation of single cell similarity maps"
DOI: 10.1038/s41467-019-12235-0, Published: 2019-09-26, Citations: 199
Preprints
"PhyloVision: Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and Phylogenetic Data"
DOI: 10.1101/2021.09.13.460142, Citations: 1
"Functional Interpretation of Single-Cell Similarity Maps"
DOI: 10.1101/403055, Citations: 7

Platform: R
Code: https://github.com/YosefLab/VISION
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Classification, Dimensionality Reduction, Gene Sets, Interactive, Visualisation
Added: 2018-12-08, Updated: 2022-05-06

visnormsc

visnormsc is a Graphical User Interface (GUI) for normalization of single-cell RNA sequencing (RNA-seq) data.

Publications: 1, Preprints: 0, Total citations: 1

Publications
"visnormsc: A Graphical User Interface to Normalize Single-cell RNA Sequencing Data"
DOI: 10.1007/s12539-017-0277-9, Published: 2017-12-26, Citations: 1

Platform: Python
Code: https://github.com/solo7773/visnormsc
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Interactive, Normalisation, Visualisation
Added: 2018-01-09, Updated: 2018-01-09

Vitessce

A framework for integrative visualization of multi-modal single-cell data
Platform: Javascript
Code: https://github.com/vitessce/vitessce
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Interactive, Visualisation
Added: 2021-02-19, Updated: 2021-06-28

W

WaveCrest

WaveCrest is a statistical approach to reconstruct gene expression trajectory in single cell RNA-seq experiments with ordered conditions.

Publications: 1, Preprints: 0, Total citations: 375

Publications
"Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm"
DOI: 10.1186/s13059-016-1033-x, Published: 2016-08-17, Citations: 375

Platform: R
Code: https://github.com/lengning/WaveCrest
starsN/A
forksN/A
last commitUnknown
License: Apache-2.0
Categories: Expression Patterns, Interactive, Marker Genes, Ordering
Added: 2016-09-12, Updated: 2016-09-12

WEDGE

WEDGE is a weighted low-rank matrix completion algorithm for recovering scRNA-seq gene expression data with high dropout rate.

Publications: 1, Preprints: 1, Total citations: 17

Publications
"WEDGE: imputation of gene expression values from single-cell RNA-seq datasets using biased matrix decomposition"
DOI: 10.1093/bib/bbab085, Published: 2021-04-08, Citations: 16
Preprints
"WEDGE: recovery of gene expression values for sparse single-cell RNA-seq datasets using matrix decomposition"
DOI: 10.1101/864488, Citations: 1

Platform: MATLAB
Code: https://github.com/QuKunLab/WEDGE
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Imputation, Interactive
Added: 2019-12-11, Updated: 2019-12-11

Wishbone

Wishbone is an algorithm to align single cells from differentiation systems with bifurcating branches.

Publications: 1, Preprints: 0, Total citations: 532

Publications
"Wishbone identifies bifurcating developmental trajectories from single-cell data"
DOI: 10.1038/nbt.3569, Published: 2016-05-02, Citations: 532

Platform: Python
Code: https://github.com/ManuSetty/wishbone
starsN/A
forksN/A
last commitUnknown
License: GPL-2.0
Categories: Expression Patterns, Interactive, Ordering, Visualisation
Added: 2016-09-09, Updated: 2020-03-12

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