scRNA-tools

A

Anchored-Fusion

Anchored-fusion is a bioinformatic tool which detects fusion genes bases on paired-end RNA-sequence with ultrahigh sensitivity

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

Publications
"Anchored-fusion enables targeted fusion search in bulk and single-cell RNA sequencing data"
DOI: 10.1016/j.crmeth.2024.100733, Published: 2024-03, Citations: 1

Platform: Python
Code: https://github.com/ShenLab-Genomics/Anchored-Fusion
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License: GPL-3.0
Categories: Variants
Added: 2024-03-22, Updated: 2024-03-22

B

badger

Bayesian approach for detecting copy number alterations from single cell RNA-seq data
Platform: R
Code: https://github.com/JEFworks/badger
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Categories: Variants, Visualisation
Added: 2017-06-05, Updated: 2017-06-05

C

CACTUS

Clonal Architecture of genomic Clustering of TUmor Single cells

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

Publications
"CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"
DOI: 10.1186/s13073-021-00842-w, Published: 2021-03-24, Citations: 4
Preprints
"CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"
DOI: 10.1101/2020.06.05.134452, Citations: 0

Platform: R
Code: https://github.com/LUMC/CACTUS
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Categories: Variants
Added: 2020-06-26, Updated: 2020-06-26

CAISC

CAISC, which stands for Clonal Architecture with Integration of SNV and CNV, is a software that integrates copy number variation and single nucleotide mutations for genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

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

Publications
"CAISC: A software to integrate copy number variations and single nucleotide mutations for genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing"
DOI: 10.1186/s12859-022-04625-x, Published: 2022-03-21, Citations: 1

Platform: R
Code: https://github.com/lizamathews/CAISC
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Categories: Clustering, Integration, Variants, Visualisation
Added: 2022-05-01, Updated: 2022-05-01

Canopy2

An R package that uses Bayesian and computational methods to infer the tumor phylogenetic tree from bulk DNA whole exome sequencing (WES) and single-cell RNA sequencing (scRNA-seq)

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

Preprints
"Canopy2: tumor phylogeny inference by bulk DNA and single-cell RNA sequencing"
DOI: 10.1101/2024.03.18.585595, Citations: 1

Platform: R
Code: https://github.com/annweideman/canopy2
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License: MIT
Categories: Ordering, Simulation, Variants, Visualisation
Added: 2024-03-22, Updated: 2024-03-22

CanSig

Discovering de novo shared transcriptional programs in single cancer cells

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

Preprints
"CanSig: discovery of shared transcriptional states across cancer patients from single-cell RNA sequencing data"
DOI: 10.1101/2022.04.14.488324, Citations: 2

Platform: Python
Code: https://github.com/BoevaLab/CanSig-Supplementary-Information
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License: MIT
Categories: Clustering, Gene Sets, Integration, Variants, Visualisation
Added: 2023-01-20, Updated: 2025-01-30

cardelino

Methods to infer clonal structure for a population of cells using single-cell RNA-seq data

Publications: 1, Preprints: 1, Total citations: 74

Publications
"Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes"
DOI: 10.1038/s41592-020-0766-3, Published: 2020-03-16, Citations: 61
Preprints
"Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants"
DOI: 10.1101/413047, Citations: 13

Platform: R
Code: https://github.com/single-cell-genetics/cardelino
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License: GPL-3.0-or-later
Categories: Classification, Simulation, Variants, Visualisation
Added: 2018-07-18, Updated: 2022-11-04

CaSpER

Identify large-scale CNV events from single cell or bulk RNA-Seq data

Publications: 1, Preprints: 0, Total citations: 117

Publications
"CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data"
DOI: 10.1038/s41467-019-13779-x, Published: 2020-01-03, Citations: 117

Platform: R
Code: https://github.com/akdess/CaSpER
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Categories: Variants, Visualisation
Added: 2020-01-13, Updated: 2020-01-13

cb_sniffer

Mutation barcode caller, calls mutant and ref barcodes from 10x single cell data

Publications: 1, Preprints: 1, Total citations: 173

Publications
"A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing"
DOI: 10.1038/s41467-019-11591-1, Published: 2019-08-14, Citations: 169
Preprints
"Mutation detection in thousands of acute myeloid leukemia cells using single cell RNA-sequencing"
DOI: 10.1101/434746, Citations: 4

Platform: Python
Code: https://github.com/sridnona/cb_sniffer
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License: GPL-3.0
Categories: Variants
Added: 2018-10-29, Updated: 2021-06-28

CCLONE

This package provides functions for analyis of single-cell variant call data

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

Preprints
"Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data"
DOI: 10.1101/2024.02.21.581377, Citations: 1

Platform: Python
Code: https://github.com/ValerieMarot/clonal_tracing_package
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Categories: Variants, Visualisation
Added: 2024-03-01, Updated: 2024-03-01

CellaRepertorium

Methods to cluster and analyze high-throughput single cell immune cell repertoires, especially from the 10X Genomics VDJ solution
Platform: R/C++
Code: https://github.com/amcdavid/CellaRepertorium
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License: GPL-3.0
Categories: Clustering, Immune, Quality Control, Variants, Visualisation
Added: 2020-11-29, Updated: 2020-11-29

CellRegMap

Cellular Regulatory Map, a linear mixed model approach to perform multi-context eQTL mapping leveraging single cell RNA sequencing (scRNA-seq) data

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

Publications
"CellRegMap: a statistical framework for mapping context‐specific regulatory variants using scRNA‐seq"
DOI: 10.15252/msb.202110663, Published: 2022-08, Citations: 34
Preprints
"CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq"
DOI: 10.1101/2021.09.01.458524, Citations: 3

Platform: Python
Code: https://github.com/limix/CellRegMap
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License: MIT
Categories: Simulation, Variants
Added: 2021-09-03, Updated: 2022-08-26

cellSNP

cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data
Platform: Python
Code: https://github.com/single-cell-genetics/cellSNP
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License: Apache-2.0
Categories: Variants
Added: 2020-01-08, Updated: 2020-01-08

cellsnp-lite

cellsnp-lite aims to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data

Publications: 1, Preprints: 1, Total citations: 115

Publications
"Cellsnp-lite: an efficient tool for genotyping single cells"
DOI: 10.1093/bioinformatics/btab358, Published: 2021-05-08, Citations: 103
Preprints
"Cellsnp-lite: an efficient tool for genotyping single cells"
DOI: 10.1101/2020.12.31.424913, Citations: 12

Platform: C/Shell/Python/R
Code: https://github.com/single-cell-genetics/cellsnp-lite
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License: Apache-2.0
Categories: Variants
Added: 2021-01-08, Updated: 2021-01-08

Chloris

A Bayesian model to utilize single-cell RNA sequencing (scRNA-seq) data for automatic analysis of intra-tumoral clonal structure with respect to CNAs

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

Preprints
"Bayesian inference for copy number intra-tumoral heterogeneity from single-cell RNA-sequencing data"
DOI: 10.1101/2023.10.22.563455, Citations: 0

Platform: R
Code: https://github.com/pqiao29/Chloris
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License: MIT
Categories: Simulation, Variants, Visualisation
Added: 2023-11-03, Updated: 2023-11-03

clonealign

clonealign assigns single-cell RNA-seq expression to cancer clones by mapping RNA-seq to clone-specific copy number profiles

Publications: 1, Preprints: 1, Total citations: 103

Publications
"clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers"
DOI: 10.1186/s13059-019-1645-z, Published: 2019-03-12, Citations: 103
Preprints
"clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers"
DOI: 10.1101/344309, Citations: 0

Platform: R
Code: https://github.com/kieranrcampbell/clonealign
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License: Apache-2.0
Categories: Integration, Variants, Visualisation
Added: 2018-05-01, Updated: 2019-03-15

ClonoCluster

A method for using clonal origin to inform transcriptome clustering

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

Publications
"ClonoCluster: A method for using clonal origin to inform transcriptome clustering"
DOI: 10.1016/j.xgen.2022.100247, Published: 2023-02, Citations: 12
Preprints
"ClonoCluster: a method for using clonal origin to inform transcriptome clustering"
DOI: 10.1101/2022.02.11.480077, Citations: 3

Platform: R
Code: https://github.com/leeprichman/ClonoCluster
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License: GPL-3.0
Categories: Clustering, Dimensionality Reduction, Marker Genes, Variants, Visualisation
Added: 2022-02-18, Updated: 2023-05-12

CONGAS

A set of Pyro models and functions to infer CNA from scRNA-seq data

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

Publications
"A Bayesian method to cluster single-cell RNA sequencing data using Copy Number Alterations"
DOI: 10.1093/bioinformatics/btac143, Published: 2022-03-17, Citations: 9
Preprints
"A Bayesian method to cluster single-cell RNA sequencing data using Copy Number Alterations"
DOI: 10.1101/2021.02.02.429335, Citations: 2

Platform: Python
Code: https://github.com/caravagnalab/congas
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License: GPL-3.0
Categories: Variants
Added: 2021-02-05, Updated: 2023-04-06

CONGASp

A set of Pyro models and functions to infer CNA from scRNA-seq and scATAC-seq data

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

Publications
"A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing"
DOI: 10.1371/journal.pcbi.1011557, Published: 2023-11-02, Citations: 2
Preprints
"A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing"
DOI: 10.1101/2023.04.01.535197, Citations: 0

Platform: Python
Code: https://github.com/caravagnalab/CONGASp
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License: GPL-3.0
Categories: Variants
Added: 2023-04-06, Updated: 2024-01-05

CONICS

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing

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

Publications
"CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones"
DOI: 10.1093/bioinformatics/bty316, Published: 2018-04-20, Citations: 94

Platform: R/Python
Code: https://github.com/diazlab/CONICS
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Categories: Integration, Variants, Visualisation
Added: 2018-05-01, Updated: 2018-05-01

CopyKAT

Inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data

Publications: 1, Preprints: 0, Total citations: 469

Publications
"Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes"
DOI: 10.1038/s41587-020-00795-2, Published: 2021-01-18, Citations: 469

Platform: R
Code: https://github.com/navinlabcode/copykat
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License: GPL-2.0
Categories: Variants
Added: 2021-10-18, Updated: 2021-10-18

copyVAE

A variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics

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

Publications
"CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics"
DOI: 10.1093/bioinformatics/btae284, Published: 2024-04-27, Citations: 0

Platform: Python
Code: https://github.com/kurtsemih/copyVAE
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License: MIT
Categories: Variants
Added: 2024-05-06, Updated: 2024-05-06

CTAT-LR-fusion

Find fusion transcripts using minimap2 and FusionInspector for long (and optionally additional short) RNA-seq reads

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

Preprints
"CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution"
DOI: 10.1101/2024.02.24.581862, Citations: 0

Platform: Perl/Javascript
Code: https://github.com/TrinityCTAT/CTAT-LR-fusion
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License: BSD-3-Clause
Categories: Variants, Visualisation
Added: 2024-03-01, Updated: 2024-03-01

D

de-goulash

de-goulash is a bioinformatics pipeline build in Snakemake which allows clustering mixed individuals using 10x single-cell RNA-seq

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

Publications
"Single-cell transcriptome sequencing allows genetic separation, characterization and identification of individuals in multi-person biological mixtures"
DOI: 10.1038/s42003-023-04557-z, Published: 2023-02-20, Citations: 12

Platform: Snakemake
Code: https://github.com/genid/de-goulash
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Categories: Variants
Added: 2023-02-24, Updated: 2023-02-24

Demuxafy

Demuxafy provides a simple framework for demultiplexing and classifying doublets in a wide range of droplet-based scRNA-seq captures

Publications: 1, Preprints: 1, Total citations: 26

Publications
"Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods"
DOI: 10.1186/s13059-024-03224-8, Published: 2024-04-15, Citations: 10
Preprints
"Demuxafy: Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods"
DOI: 10.1101/2022.03.07.483367, Citations: 16

Platform: Singularity/R/Python
Code: https://github.com/drneavin/Demultiplexing_Doublet_Detecting_Docs
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License: MIT
Categories: Quality Control, Variants
Added: 2022-03-11, Updated: 2024-04-26

Demuxalot

Reliable and efficient idenfitication of genotypes for individual cells in RNA sequencing that refines the knowledge about genotypes from the data

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

Preprints
"Demuxalot: scaled up genetic demultiplexing for single-cell sequencing"
DOI: 10.1101/2021.05.22.443646, Citations: 3

Platform: Python
Code: https://github.com/herophilus/demuxalot
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License: MIT
Categories: Variants
Added: 2021-05-28, Updated: 2021-06-04

demuxlet

Genetic multiplexing of barcoded single cell RNA-seq

Publications: 1, Preprints: 1, Total citations: 895

Publications
"Multiplexed droplet single-cell RNA-sequencing using natural genetic variation"
DOI: 10.1038/nbt.4042, Published: 2017-12-11, Citations: 885
Preprints
"Multiplexing droplet-based single cell RNA-sequencing using natural genetic barcodes"
DOI: 10.1101/118778, Citations: 10

Platform: C++
Code: https://github.com/statgen/demuxlet
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License: Apache-2.0
Categories: Quality Control, UMIs, Variants
Added: 2017-03-29, Updated: 2018-03-14

DENDRO

DENDRO, stands for Dna based EvolutioNary tree preDiction by scRna-seq technOlogy, is an R package, which takes scRNA-seq data for a tumor (or related somatic tissues) and accurately reconstructs its phylogeny, assigning each single cell from the single cell RNA sequencing (scRNA-seq) data to a subclone.

Publications: 1, Preprints: 1, Total citations: 44

Publications
"DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing"
DOI: 10.1186/s13059-019-1922-x, Published: 2020-01-14, Citations: 43
Preprints
"Genetic Heterogeneity Profiling by Single Cell RNA Sequencing"
DOI: 10.1101/457622, Citations: 1

Platform: R
Code: https://github.com/zhouzilu/DENDRO
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License: GPL-3.0
Categories: Clustering, Simulation, Variants, Visualisation
Added: 2018-11-14, Updated: 2020-01-22

E

EPIC

EPIC (cEll tyPe enrIChment), a statistical framework that relates large-scale GWAS summary statistics to cell-type-specific omics measurements from single-cell sequencing

Publications: 1, Preprints: 1, Total citations: 14

Publications
"EPIC: Inferring relevant cell types for complex traits by integrating genome-wide association studies and single-cell RNA sequencing"
DOI: 10.1371/journal.pgen.1010251, Published: 2022-06-16, Citations: 12
Preprints
"EPIC: inferring relevant cell types for complex traits by integrating genome-wide association studies and single-cell RNA sequencing"
DOI: 10.1101/2021.06.09.447805, Citations: 2

Platform: R
Code: https://github.com/rujinwang/EPIC
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License: GPL-2.0
Categories: Variants, Visualisation
Added: 2021-06-25, Updated: 2022-06-17

eQTLsingle

eQTLsingle is an R package for discovering eQTLs only with single cell RNA-seq (scRNA-seq) data, without genomic data

Publications: 1, Preprints: 1, Total citations: 10

Publications
"Discovering single-cell eQTLs from scRNA-seq data only"
DOI: 10.1016/j.gene.2022.146520, Published: 2022-06, Citations: 8
Preprints
"Discovering single-cell eQTLs from scRNA-seq data only"
DOI: 10.1101/2021.06.10.447906, Citations: 2

Platform: R/Shell
Code: https://github.com/horsedayday/eQTLsingle
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Categories: Alignment, Quantification, Variants
Added: 2021-06-11, Updated: 2022-04-30

F

FLAMES

A computational framework to perform single-cell full-length analysis of mutations and splicing

Publications: 1, Preprints: 1, Total citations: 137

Publications
"Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing"
DOI: 10.1186/s13059-021-02525-6, Published: 2021-11-11, Citations: 122
Preprints
"Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing"
DOI: 10.1101/2020.08.10.243543, Citations: 15

Platform: Python/C/C++/R
Code: https://github.com/LuyiTian/FLAMES
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License: GPL-3.0
Categories: Alignment, Quantification, UMIs, Variants
Added: 2020-08-20, Updated: 2021-11-27

Flexiplex

Flexiplex is a lightweight, flexible, error-tolerant search, and demultiplexing tool

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

Publications
"Flexiplex: a versatile demultiplexer and search tool for omics data"
DOI: 10.1093/bioinformatics/btae102, Published: 2024-02-21, Citations: 3
Preprints
"Flexiplex: A versatile demultiplexer and search tool for omics data"
DOI: 10.1101/2023.08.21.554084, Citations: 1

Platform: C++/C
Code: https://github.com/DavidsonGroup/flexiplex
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License: MIT
Categories: UMIs, Variants
Added: 2022-09-16, Updated: 2024-05-06

G

genomicInstability

This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data
Platform: R
Code: https://github.com/reef103/genomicInstability
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License: Custom
Categories: Variants, Visualisation
Added: 2021-11-05, Updated: 2021-11-05

GiRAFR

GiRAFR is a python package developed to perform quality control of single cell CRISPR screens, and to assign gRNAs to cells in a sensitive, mutation-aware manner

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

Publications
"GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens"
DOI: 10.1038/s42003-023-05351-7, Published: 2023-09-23, Citations: 2
Preprints
"GiRAFR improves gRNA detection and annotation in single cell CRISPR screens"
DOI: 10.1101/2022.10.24.513352, Citations: 0

Platform: Python
Code: https://github.com/FunctionalEpigeneticsLab/GiRAFR
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License: MIT
Categories: Quantification, UMIs, Variants
Added: 2022-10-28, Updated: 2024-01-05

GSFA

Bayesian sparse factor analysis on single-cell CRISPR screen data

Publications: 1, Preprints: 1, Total citations: 16

Publications
"A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening"
DOI: 10.1038/s41592-023-02017-4, Published: 2023-09-28, Citations: 15
Preprints
"A novel Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening"
DOI: 10.1101/2022.02.13.480282, Citations: 1

Platform: R/C++
Code: https://github.com/xinhe-lab/GSFA
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License: MIT
Categories: Normalisation, Perturbations, Variable Genes, Variants
Added: 2022-02-18, Updated: 2023-10-27

H

HiScanner

HiScanner is a lightweight python package for high-resolution single-cell copy number analysis

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

Preprints
"High-resolution detection of copy number alterations in single cells with HiScanner"
DOI: 10.1101/2024.04.26.587806, Citations: 0

Platform: C/Python/R/Perl
Code: https://github.com/parklab/HiScanner
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License: MIT
Categories: Variants
Added: 2024-05-06, Updated: 2024-05-06

HoneyBADGER

hidden Markov model integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

Publications: 1, Preprints: 0, Total citations: 194

Publications
"Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data"
DOI: 10.1101/gr.228080.117, Published: 2018-06-13, Citations: 194

Platform: R
Code: https://github.com/JEFworks/HoneyBADGER
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License: GPL-3.0
Categories: Variants, Visualisation
Added: 2018-04-17, Updated: 2018-06-27

HTOreader

An R toolkit for cell hashing (HTO) demultiplexing

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

Preprints
"A hybrid single-cell demultiplexing strategy that increases both cell recovery rate and calling accuracy"
DOI: 10.1101/2023.04.02.535299, Citations: 4

Platform: R
Code: https://github.com/WilsonImmunologyLab/HTOreader
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License: GPL-3.0
Categories: Quantification, Variants, Visualisation
Added: 2023-04-06, Updated: 2023-04-06

I

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

ikarus

Ikarus is a stepwise machine learning pipeline that tries to cope with a task of distinguishing tumor cells from normal cells

Publications: 1, Preprints: 1, Total citations: 39

Publications
"Identifying tumor cells at the single-cell level using machine learning"
DOI: 10.1186/s13059-022-02683-1, Published: 2022-05-30, Citations: 37
Preprints
"Identifying tumor cells at the single cell level"
DOI: 10.1101/2021.10.15.463909, Citations: 2

Platform: Python
Code: https://github.com/BIMSBbioinfo/ikarus
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License: MIT
Categories: Classification, Variants
Added: 2021-10-22, Updated: 2022-06-17

inferCNV

Infer Copy Number Variation using Single-cell RNA-Seq Expression Data.

Publications: 1, Preprints: 0, Total citations: 3813

Publications
"Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma"
DOI: 10.1126/science.1254257, Published: 2014-06-12, Citations: 3813

Platform: R
Code: https://github.com/broadinstitute/inferCNV
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Categories: Variants, Visualisation
Added: 2018-02-22, Updated: 2018-02-22

inferCNVpy

Infercnv is a scalable python library to infer copy number variation (CNV) events from single cell transcriptomics data. It is heavliy inspired by InferCNV, but plays nicely with scanpy and is much more scalable.
Platform: Python
Code: https://github.com/icbi-lab/infercnvpy
starsN/A
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last commitUnknown
License: BSD-3-Clause
Categories: Clustering, Dimensionality Reduction, Variants
Added: 2021-02-12, Updated: 2021-02-12

IronThrone-GoT

Processes GoT amplicon data and generates a table of metrics

Publications: 1, Preprints: 1, Total citations: 249

Publications
"Somatic mutations and cell identity linked by Genotyping of Transcriptomes"
DOI: 10.1038/s41586-019-1367-0, Published: 2019-07-03, Citations: 244
Preprints
"High throughput droplet single-cell Genotyping of Transcriptomes (GoT) reveals the cell identity dependency of the impact of somatic mutations"
DOI: 10.1101/444687, Citations: 5

Platform: Perl
Code: https://github.com/landau-lab/IronThrone-GoT
starsN/A
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last commitUnknown
Categories: UMIs, Variants
Added: 2019-07-04, Updated: 2019-07-04

L

LINEAGE

Label-free IdeNtification of Endogenous informAtive sinGle cell mitochondrial RNA mutation for lineage analysis and clonal Evolution (LINEAGE)

Publications: 1, Preprints: 0, Total citations: 9

Publications
"LINEAGE: Label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis"
DOI: 10.1073/pnas.2119767119, Published: 2022-01-27, Citations: 9

Platform: R
Code: https://github.com/songjiajia2018/LINEAGE
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last commitUnknown
License: GPL-3.0
Categories: Marker Genes, Ordering, Variants
Added: 2022-02-04, Updated: 2022-02-04

M

MaCroDNA

MaCroDNA (Matching Cross-Domain Nucleic Acids) is a correlation-based method to perform mapping between scRNA-seq gene expression and scDNA-seq copy number values

Publications: 1, Preprints: 1, Total citations: 6

Publications
"Accurate integration of single-cell DNA and RNA for analyzing intratumor heterogeneity using MaCroDNA"
DOI: 10.1038/s41467-023-44014-3, Published: 2023-12-13, Citations: 5
Preprints
"MaCroDNA: Accurate integration of single-cell DNA and RNA data for a deeper understanding of tumor heterogeneity"
DOI: 10.1101/2022.08.21.504709, Citations: 1

Platform: Python
Code: https://github.com/NakhlehLab/MaCroDNA
starsN/A
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last commitUnknown
Categories: Integration, Variants
Added: 2023-02-17, Updated: 2024-01-05

MEDALT

This package performs lineage tracing using copy number profile from single cell sequencing technology

Publications: 1, Preprints: 1, Total citations: 24

Publications
"MEDALT: single-cell copy number lineage tracing enabling gene discovery"
DOI: 10.1186/s13059-021-02291-5, Published: 2021-02-23, Citations: 23
Preprints
"Single-cell copy number lineage tracing enabling gene discovery"
DOI: 10.1101/2020.04.12.038281, Citations: 1

Platform: Python/R
Code: https://github.com/KChen-lab/MEDALT
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last commitUnknown
License: MIT
Categories: Ordering, Variants
Added: 2020-04-14, Updated: 2021-03-05

MitoHEAR

MitoHEAR (Mitochondrial HEteroplasmy AnalyzeR) is an R package that allows the estimation as well as downstream statistical analysis of the mtDNA heteroplasmy calculated from single-cell datasets

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

Publications
"MitoHEAR: an R package for the estimation and downstream statistical analysis of the mitochondrial DNA heteroplasmy calculated from single-cell datasets"
DOI: 10.21105/joss.04265, Published: 2022-06-01, Citations: 0

Platform: R
Code: https://github.com/ScialdoneLab/MitoHEAR
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Clustering, Variants, Visualisation
Added: 2022-06-10, Updated: 2022-06-10

MitoTrace

MitoTrace, a user-friendly R package for the analysis of mitochondrial variation in next generation sequencing data

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

Publications
"MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data"
DOI: 10.3390/genes14061222, Published: 2023-06-04, Citations: 2

Platform: R
Code: https://github.com/lkmklsmn/MitoTrace
starsN/A
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last commitUnknown
License: GPL-2.0-or-later
Categories: Quantification, Variants
Added: 2023-06-30, Updated: 2023-06-30

Monopogen

Monopogen is an analysis package for population analysis from single-cell sequencing

Publications: 1, Preprints: 1, Total citations: 16

Publications
"Single-nucleotide variant calling in single-cell sequencing data with Monopogen"
DOI: 10.1038/s41587-023-01873-x, Published: 2023-08-17, Citations: 16
Preprints
"Monopogen: single nucleotide variant calling from single cell sequencing"
DOI: 10.1101/2022.12.04.519058, Citations: 0

Platform: Python
Code: https://github.com/KChen-lab/Monopogen
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Variants
Added: 2022-12-09, Updated: 2024-02-02

MQuad

MQuad: Mixture Model for Mitochondrial Mutation detection in single-cell omics data

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

Publications
"MQuad enables clonal substructure discovery using single cell mitochondrial variants"
DOI: 10.1038/s41467-022-28845-0, Published: 2022-03-08, Citations: 25
Preprints
"MQuad enables clonal substructure discovery using single cell mitochondrial variants"
DOI: 10.1101/2021.03.27.437331, Citations: 0

Platform: Python
Code: https://github.com/single-cell-genetics/MQuad
starsN/A
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last commitUnknown
License: Apache-2.0
Categories: Variants, Visualisation
Added: 2021-04-05, Updated: 2022-04-30

MSIsensor-RNA

MSIsensor-RNA is a member of MSIsensor family for microsatellite instability (MSI) detection using RNA expression data including Microarray, RNA-seq, and single RNA-seq

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

Publications
"MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data"
DOI: 10.1093/gpbjnl/qzae004, Published: 2024-01-10, Citations: 2
Preprints
"MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data"
DOI: 10.1101/2023.10.09.561613, Citations: 0

Platform: Python
Code: https://github.com/xjtu-omics/msisensor-rna
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last commitUnknown
License: Custom
Categories: Variants
Added: 2023-10-27, Updated: 2024-05-06

N

NOMAD

A statistical, reference-free algorithm subsumes myriad problems in genome science and enables novel discovery

Publications: 0, Preprints: 1, Total citations: 6

Preprints
"Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells"
DOI: 10.1101/2022.12.06.519414, Citations: 6

Platform: Python/Nextflow/Groovy
Code: https://github.com/salzman-lab/nomad
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last commitUnknown
License: MIT
Categories: Alternative Splicing, Variants
Added: 2022-12-09, Updated: 2022-12-09

NOMAD2

NOMAD is an unsupervised and reference-free unifying framework to discover regulated sequence variation through statistical analysis of k-mer composition in both DNA and RNA sequence

Publications: 0, Preprints: 1, Total citations: 6

Preprints
"SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads"
DOI: 10.1101/2023.03.17.533189, Citations: 6

Platform: C++/C/Python/R
Code: https://github.com/refresh-bio/NOMAD
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Alternative Splicing, Variants
Added: 2023-03-24, Updated: 2024-10-29

O

Originiator

Computational Framework Separating Single-Cell RNA-Seq by Genetic and Contextual Information

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

Preprints
"Originator: Computational Framework Separating Single-Cell RNA-Seq by Genetic and Contextual Information"
DOI: 10.1101/2024.04.04.588144, Citations: 0

Platform: R
Code: https://github.com/lanagarmire/Originator
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last commitUnknown
License: MIT
Categories: Immune, Quality Control, Variants
Added: 2024-04-12, Updated: 2025-01-30

P

PhylEx

Integrated analysis of bulk aDNA-seq and single cell RNA-seq data

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

Preprints
"PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data"
DOI: 10.1101/2021.02.16.431009, Citations: 1

Platform: C++
Code: https://github.com/junseonghwan/PhylEx
starsN/A
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last commitUnknown
Categories: Integration, Variants
Added: 2021-02-19, Updated: 2021-02-19

phyloRNA

phyloRNA is an utility package that maps functionality of a commonly used software to easy building phylogenetic trees from scRNAseq data

Publications: 1, Preprints: 1, Total citations: 14

Publications
"Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data"
DOI: 10.1089/cmb.2022.0357, Published: 2022-12-06, Citations: 4
Preprints
"Cancer phylogenetics using single-cell RNA-seq data"
DOI: 10.1101/2021.01.07.425804, Citations: 10

Platform: R/Python
Code: https://github.com/bioDS/phyloRNA
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last commitUnknown
License: MIT
Categories: Alignment, Normalisation, Ordering, Quality Control, Quantification, UMIs, Variants
Added: 2021-01-15, Updated: 2023-01-04

powerEQTL

Flexible functions to calculate power, minimal sample size, or detectable minor allele frequency in both bulk tissue and single-cell eQTL analysis

Publications: 1, Preprints: 1, Total citations: 22

Publications
"powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis"
DOI: 10.1093/bioinformatics/btab385, Published: 2021-05-19, Citations: 21
Preprints
"powerEQTL: An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis"
DOI: 10.1101/2020.12.15.422954, Citations: 1

Platform: R
Code: https://github.com/sterding/powerEQTL
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last commitUnknown
License: GPL-2.0-or-later
Categories: Variants
Added: 2021-01-08, Updated: 2021-01-08

R

Red_Panda

Red Panda employs the unique information found in scRNA-seq to increase accuracy of variant detection compared to software designed for bulk sequencing.

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

Publications
"Red panda: a novel method for detecting variants in single-cell RNA sequencing"
DOI: 10.1186/s12864-020-07224-3, Published: 2020-12-29, Citations: 0
Preprints
"Red Panda: A novel method for detecting variants in single-cell RNA sequencing"
DOI: 10.1101/2020.01.08.898874, Citations: 1

Platform: Perl
Code: https://github.com/adamcornish/red_panda
starsN/A
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last commitUnknown
License: MIT
Categories: Variants
Added: 2020-01-18, Updated: 2020-01-18

RESA

RESA detects somatic mutation with high precision directly from scRNA-seq data

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

Publications
"De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data"
DOI: 10.1186/s13073-023-01269-1, Published: 2023-12-18, Citations: 3
Preprints
"Detecting expressed cancer somatic mutations from single-cell RNA sequencing data"
DOI: 10.1101/2021.10.08.463191, Citations: 0

Platform: Perl/Python/Shell/R
Code: https://github.com/ShenLab-Genomics/RESA
starsN/A
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last commitUnknown
License: MIT
Categories: Variants
Added: 2024-01-05, Updated: 2024-01-05

RNA-strain-match

RNA Strain-Match uses known coding SNPs from strains to match bulk, single-cell, or nuclear RNA sequencing data to its appropriate strain

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

Preprints
"RNA Strain-Match: A tool for matching single-nucleus, single-cell, or bulk RNA-sequencing alignment data to its corresponding genotype"
DOI: 10.1101/2023.07.14.548847, Citations: 0

Platform: R/Shell
Code: https://github.com/jon-willcox/RNA-strain-match
starsN/A
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last commitUnknown
Categories: Alignment, Variants
Added: 2023-07-21, Updated: 2023-07-21

S

scAllele

scAllele is a versatile tool to detect and analyze nucleotide variants in scRNA-seq

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

Publications
"scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq"
DOI: 10.1126/sciadv.abn6398, Published: 2022-09-02, Citations: 7
Preprints
"scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq"
DOI: 10.1101/2022.03.29.486330, Citations: 0

Platform: Python
Code: https://github.com/gxiaolab/scAllele
starsN/A
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last commitUnknown
License: MIT
Categories: Alternative Splicing, Variants
Added: 2022-04-08, Updated: 2023-01-04

scDecouple

scDecouple is an R package that aims to decouple true cellular response from infected proportion bias in scCRISPR-seq

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

Publications
"scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq"
DOI: 10.1093/bib/bbae011, Published: 2024-01-22, Citations: 1
Preprints
"scDecouple: Decoupling cellular response from infected proportion bias in scCRISPR-seq"
DOI: 10.1101/2023.01.31.526445, Citations: 0

Platform: R
Code: https://github.com/MengQiuchen/scDecouple
starsN/A
forksN/A
last commitUnknown
Categories: Gene Sets, Perturbations, Variants
Added: 2023-09-08, Updated: 2024-05-06

scDRS

scDRS (single-cell disease-relevance score) is a method for associating individual cells in single-cell RNA-seq data with disease GWASs

Publications: 1, Preprints: 1, Total citations: 112

Publications
"Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data"
DOI: 10.1038/s41588-022-01167-z, Published: 2022-09-01, Citations: 111
Preprints
"Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data"
DOI: 10.1101/2021.09.24.461597, Citations: 1

Platform: Python
Code: https://github.com/martinjzhang/scDRS
starsN/A
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last commitUnknown
License: MIT
Categories: Variants
Added: 2022-03-11, Updated: 2023-01-04

SCEVAN

Easy-to-use R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells

Publications: 1, Preprints: 1, Total citations: 51

Publications
"A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data"
DOI: 10.1038/s41467-023-36790-9, Published: 2023-02-25, Citations: 46
Preprints
"A fast variational algorithm to detect the clonal copy number substructure of tumors from single-cell data"
DOI: 10.1101/2021.11.20.469390, Citations: 5

Platform: R/C
Code: https://github.com/AntonioDeFalco/SCEVAN
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Classification, Variants
Added: 2021-12-10, Updated: 2023-03-03

scFusion

scFusion is a computational pipeline for detecting gene fusions at single-cell resolution

Publications: 1, Preprints: 1, Total citations: 14

Publications
"Single-cell gene fusion detection by scFusion"
DOI: 10.1038/s41467-022-28661-6, Published: 2022-02-28, Citations: 14
Preprints
"Single cell gene fusion detection by scFusion"
DOI: 10.1101/2020.12.27.424506, Citations: 0

Platform: Python/R
Code: https://github.com/XiDsLab/scFusion
starsN/A
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last commitUnknown
License: MIT
Categories: Variants
Added: 2021-01-08, Updated: 2022-03-04

scGWAS

scGWAS leverages scRNA-seq data to identify the genetically mediated associations between traits and cell types

Publications: 1, Preprints: 0, Total citations: 21

Publications
"scGWAS: landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies"
DOI: 10.1186/s13059-022-02785-w, Published: 2022-10-17, Citations: 21

Platform: Java
Code: https://github.com/bsml320/scGWAS
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Variants
Added: 2022-10-28, Updated: 2022-10-28

SClineager

Tracing lineage of single cells via genetic variants based on a Bayesian Hierarchical model

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

Publications
"Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data"
DOI: 10.1016/j.celrep.2020.108589, Published: 2021-01, Citations: 17
Preprints
"Overcoming Genetic Drop-outs in Variants-based Lineage Tracing from Single-cell RNA Sequencing Data"
DOI: 10.1101/2020.01.01.892562, Citations: 0

Platform: R/C++
Code: https://github.com/inmybrain/SClineager
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Ordering, Variants
Added: 2020-01-08, Updated: 2021-01-15

scMAGeCK

scMAGeCK is a computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data (CROP-seq)

Publications: 1, Preprints: 2, Total citations: 58

Publications
"scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens"
DOI: 10.1186/s13059-020-1928-4, Published: 2020-01-24, Citations: 55
Preprints
"Decoding Heterogenous Single-cell Perturbation Responses"
DOI: 10.1101/2023.10.30.564796, Citations: 2
"Linking genotypes with multiple phenotypes in single-cell CRISPR screens"
DOI: 10.1101/658146, Citations: 1

Platform: R/Python
Code: https://bitbucket.org/weililab/scmageck
License: BSD-2-Clause
Categories: Perturbations, Quantification, Variants
Added: 2020-02-05, Updated: 2023-12-01

scMitoMut

A R/Bioconductor Package for Mitochondrial Mutation Analysis in Single-Cell Omics Data
Platform: R/C++
Code: https://github.com/wenjie1991/scMitoMut
starsN/A
forksN/A
last commitUnknown
License: Artistic-2.0
Categories: Variants, Visualisation
Added: 2024-05-06, Updated: 2024-05-06

SCmut

SCmut is a novel and robust statistical method for cell-level somatic mutation detection from single-cell RNA-sequencing

Publications: 1, Preprints: 0, Total citations: 39

Publications
"Cell-level somatic mutation detection from single-cell RNA sequencing"
DOI: 10.1093/bioinformatics/btz288, Published: 2019-04-26, Citations: 39

Platform: R
Code: https://github.com/nghiavtr/SCmut
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last commitUnknown
License: GPL-3.0
Categories: Variants
Added: 2019-05-07, Updated: 2019-05-07

scNanoGPS

scNanoGPS is a computational toolkit for analyzing high throughput single cell nanopore sequencing data to detect Genotypes and Phenotype Simultaneously from same cells

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

Preprints
"Delineating genotypes and phenotypes of individual cells from long-read single cell transcriptomes"
DOI: 10.1101/2023.01.24.525264, Citations: 0

Platform: Python
Code: https://github.com/gaolabtools/scNanoGPS
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Alignment, Alternative Splicing, Quantification, UMIs, Variants
Added: 2023-01-27, Updated: 2023-01-27

SComatic

SComatic is a tool that provides functionalities to detect somatic single-nucleotide mutations in high-throughput single-cell genomics and transcriptomics data sets

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

Preprints
"Accuratede novodetection of somatic mutations in high-throughput single-cell profiling data sets"
DOI: 10.1101/2022.11.22.517567, Citations: 1

Platform: Python/R
Code: https://github.com/cortes-ciriano-lab/SComatic
starsN/A
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last commitUnknown
Categories: Quantification, Variants
Added: 2022-12-02, Updated: 2022-12-02

scPagwas

scPagwas employing the polygenic regression model to uncover trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with genome-wide association studies (GWAS) data

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

Publications
"Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data"
DOI: 10.1016/j.xgen.2023.100383, Published: 2023-09, Citations: 33
Preprints
"Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data"
DOI: 10.1101/2023.03.04.23286805, Citations: 3

Platform: R
Code: https://github.com/dengchunyu/scPagwas
starsN/A
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last commitUnknown
License: MIT
Categories: Gene Networks, Variants, Visualisation
Added: 2023-03-10, Updated: 2024-01-05

scploid

To detect aneuploidies from scRNA-sequencing data we computed, for a defined group of cells, a score for each chromosome-cell pair that measures whether the expression level of genes in that chromosome differs substantially from other cells.

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

Publications
"Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data"
DOI: 10.1186/s12864-017-4253-x, Published: 2017-11-25, Citations: 23

Platform: R
Code: https://github.com/MarioniLab/Aneuploidy2017
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Variants, Visualisation
Added: 2017-12-07, Updated: 2017-12-07

SCReadCounts

SCReadCounts is a computational tool for a cell-level assessment of the read counts bearing a particular nucleotide at genomic positions of interest from single cell RNA sequencing (scRNA-seq) data

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

Publications
"SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data"
DOI: 10.1186/s12864-021-07974-8, Published: 2021-09-22, Citations: 20
Preprints
"SCReadCounts: Estimation of cell-level SNVs from scRNA-seq data"
DOI: 10.1101/2020.11.23.394569, Citations: 1

Platform: Python
Code: https://github.com/HorvathLab/NGS
starsN/A
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last commitUnknown
License: MIT
Categories: Variants
Added: 2020-11-29, Updated: 2021-09-24

scSNPdemux

Bioinformatically demultiplex samples from single cell sequencing using SNP information and genotype information

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

Publications
"scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis"
DOI: 10.1186/s12859-023-05440-8, Published: 2023-08-31, Citations: 1

Platform: Shell/R
Code: https://github.com/wkljohn/scSNPdemux
starsN/A
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last commitUnknown
License: GPL-3.0
Categories: Variants
Added: 2023-09-08, Updated: 2023-09-08

scsnv

scSNV is an alternative to Cell Ranger + velocyto for the alignment, quantification and SNV calling of 10X Single Cell RNA-seq data

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

Publications
"scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing"
DOI: 10.1186/s13059-021-02364-5, Published: 2021-05-07, Citations: 11

Platform: C++/Python
Code: https://github.com/GWW/scsnv
starsN/A
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last commitUnknown
License: MIT
Categories: Alignment, Quantification, Variants
Added: 2021-05-14, Updated: 2021-05-14

scSplit

Genotype-free demultiplexing of pooled single-cell RNAseq, using a hidden state model for identifying genetically distinct samples within a mixed population

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

Publications
"Genotype-free demultiplexing of pooled single-cell RNA-seq"
DOI: 10.1186/s13059-019-1852-7, Published: 2019-12-19, Citations: 72
Preprints
"Genotype-free demultiplexing of pooled single-cell RNA-seq"
DOI: 10.1101/570614, Citations: 4

Platform: Python
Code: https://github.com/jon-xu/sc_split
starsN/A
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last commitUnknown
License: MIT
Categories: Variants
Added: 2019-03-15, Updated: 2021-06-28

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

SiCeLoRe

SiCeLoRe (Single Cell Long Read) is a suite of tools dedicated to cell barcode / UMI assignment and bioinformatics analysis of highly multiplexed single cell Nanopore long read sequencing data.

Publications: 1, Preprints: 1, Total citations: 164

Publications
"High throughput error corrected Nanopore single cell transcriptome sequencing"
DOI: 10.1038/s41467-020-17800-6, Published: 2020-08-12, Citations: 158
Preprints
"High throughput, error corrected Nanopore single cell transcriptome sequencing"
DOI: 10.1101/831495, Citations: 6

Platform: Java
Code: https://github.com/ucagenomix/sicelore
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Allele Specific, Alternative Splicing, UMIs, Variants
Added: 2020-03-25, Updated: 2020-03-25

souporcell

souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.

Publications: 1, Preprints: 1, Total citations: 348

Publications
"Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes"
DOI: 10.1038/s41592-020-0820-1, Published: 2020-05-04, Citations: 334
Preprints
"souporcell: Robust clustering of single cell RNAseq by genotype and ambient RNA inference without reference genotypes"
DOI: 10.1101/699637, Citations: 14

Platform: Python/Rust
Code: https://github.com/wheaton5/souporcell
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Clustering, Quality Control, Variants
Added: 2019-07-15, Updated: 2020-05-14

SPLASH

SPLASH is an unsupervised and reference-free unifying framework to discover regulated sequence variation through statistical analysis of k-mer composition in both DNA and RNA sequence

Publications: 0, Preprints: 1, Total citations: 6

Preprints
"SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads"
DOI: 10.1101/2023.03.17.533189, Citations: 6

Platform: C++/Python/R
Code: https://github.com/refresh-bio/SPLASH
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Alternative Splicing, Quantification, Variants
Added: 2024-04-05, Updated: 2024-10-29

SSrGE

This procedure aims to fit sparse linear models using a binary matrix (n_samples x n_SNV) as features matrix and a gene expression matrix (n_genes x n_samples) as response.

Publications: 1, Preprints: 1, Total citations: 57

Publications
"Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage"
DOI: 10.1038/s41467-018-07170-5, Published: 2018-11-20, Citations: 52
Preprints
"Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Subpopulations and Genotype-phenotype Linkage"
DOI: 10.1101/095810, Citations: 5

Platform: Python
Code: https://github.com/lanagarmire/SSrGE
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Clustering, Integration, Variants
Added: 2017-01-10, Updated: 2018-12-01

SURGE

A probabilistic model that attempts to uncover context specific expression quantitative trait loci (eQTLs) withouth pre-specifying contexts of interest

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

Publications
"SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models"
DOI: 10.1186/s13059-023-03152-z, Published: 2024-01-22, Citations: 6
Preprints
"Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models"
DOI: 10.1101/2022.12.22.521678, Citations: 1

Platform: Python
Code: https://github.com/BennyStrobes/surge
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Gene Networks, Variants
Added: 2024-02-02, Updated: 2024-02-02

T

TBSP

TBSP: Trajectory Inference Based on SNP information

Publications: 1, Preprints: 1, Total citations: 22

Publications
"Cell lineage inference from SNP and scRNA-Seq data"
DOI: 10.1093/nar/gkz146, Published: 2019-03-01, Citations: 18
Preprints
"Cell lineage inference from SNP and scRNA-Seq data"
DOI: 10.1101/401943, Citations: 4

Platform: Python
Code: https://github.com/phoenixding/tbsp
starsN/A
forksN/A
last commitUnknown
Categories: Clustering, Ordering, Variants, Visualisation
Added: 2018-11-13, Updated: 2018-11-13

V

VarTrix

VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data.
Platform: Rust
Code: https://github.com/10XGenomics/vartrix
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Alignment, Variants
Added: 2018-09-14, Updated: 2018-09-14

Vireo

Vireo: Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data

Publications: 1, Preprints: 1, Total citations: 217

Publications
"Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference"
DOI: 10.1186/s13059-019-1865-2, Published: 2019-12-13, Citations: 212
Preprints
"Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference"
DOI: 10.1101/598748, Citations: 5

Platform: Python
Code: https://github.com/single-cell-genetics/vireo
starsN/A
forksN/A
last commitUnknown
License: Apache-2.0
Categories: Variants
Added: 2020-01-08, Updated: 2020-01-08

X

XClone

Inference of Clonal Copy Number Variation in Single Cells

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

Preprints
"XClone: detection of allele-specific subclonal copy number variations from single-cell transcriptomic data"
DOI: 10.1101/2023.04.03.535352, Citations: 1

Platform: Python
Code: https://github.com/single-cell-genetics/XClone
starsN/A
forksN/A
last commitUnknown
License: Apache-2.0
Categories: Variants, Visualisation
Added: 2023-04-06, Updated: 2023-04-06

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