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B

bonvoyage

Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction.

Publications: 1, Preprints: 0, Total citations: 164

Publications
"Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation"
DOI: 10.1016/j.molcel.2017.06.003, Published: 2017-07, Citations: 164

Platform: Python
Code: https://github.com/yeolab/bonvoyage
starsN/A
forksN/A
last commitUnknown
License: BSD-3-Clause
Categories: Transformation
Added: 2016-09-08, Updated: 2017-07-16

C

cell2sentence

Reframing cells as sentences of genes, ordered by expression

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

Preprints
"Representing cells as sentences enables natural-language processing for single-cell transcriptomics"
DOI: 10.1101/2022.09.18.508438, Citations: 2

Platform: Python
Code: https://github.com/rahuldhodapkar/cell2sentence
starsN/A
forksN/A
last commitUnknown
License: CC-BY-NC-SA-4.0
Categories: Transformation
Added: 2023-10-20, Updated: 2023-10-20

cell2sentence-ft

Cell2Sentence is a novel method for adapting large language models to single-cell transcriptomics

Publications: 0, Preprints: 1, Total citations: 8

Preprints
"Cell2Sentence: Teaching Large Language Models the Language of Biology"
DOI: 10.1101/2023.09.11.557287, Citations: 8

Platform: Python
Code: https://github.com/vandijklab/cell2sentence-ft
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Transformation
Added: 2023-10-20, Updated: 2023-10-20

D

dsb

An R package for normalizing and denoising antibody derived tag (ADT) data from CITE-seq and derivative assays (TEA-seq, ASAP-seq etc.)

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

Publications
"Normalizing and denoising protein expression data from droplet-based single cell profiling"
DOI: 10.1038/s41467-022-29356-8, Published: 2022-04-19, Citations: 93
Preprints
"Normalizing and denoising protein expression data from droplet-based single cell profiling"
DOI: 10.1101/2020.02.24.963603, Citations: 19

Platform: R
Code: https://github.com/niaid/dsb
starsN/A
forksN/A
last commitUnknown
License: Custom
Categories: Immune, Normalisation, Transformation
Added: 2021-03-05, Updated: 2023-03-31

F

FeatureCorr

An R package to study feature correlations aided with data transformation for Next Generation sequencing and microarray data

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

Publications
"FeatureCorr: An R package to study feature correlations aided with data transformation for sequencing and microarray data"
DOI: 10.1016/j.simpa.2021.100144, Published: 2021-11, Citations: 1

Platform: R
Code: https://github.com/DKundnani/FeatureCorr
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Transformation, Visualisation
Added: 2021-10-02, Updated: 2021-10-02

Fotomics

Fotomics: Fourier transform-based omics imagification for deep learning-based cell-identity mapping using single-cell omics profiles

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

Publications
"Fotomics: fourier transform-based omics imagification for deep learning-based cell-identity mapping using single-cell omics profiles"
DOI: 10.1007/s10462-022-10357-4, Published: 2022-12-09, Citations: 1
Preprints
"Fotomics: Fourier transform-based omics imagification for deep learning-based cell-identity mapping using single-cell omics profiles"
DOI: 10.1101/2022.07.08.499309, Citations: 0

Platform: Python
Code: https://github.com/VafaeeLab/Fotomics-Imagification
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Normalisation, Transformation
Added: 2022-12-16, Updated: 2022-12-16

G

GeneSwitches

The goal of GeneSwitches is to discover the order of gene-expression and functional events during cell state transitions at a single-cell resolution.

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

Preprints
"GeneSwitches : Ordering gene-expression and functional events in single-cell experiments"
DOI: 10.1101/832626, Citations: 0

Platform: R
Code: https://github.com/SGDDNB/GeneSwitches
starsN/A
forksN/A
last commitUnknown
Categories: Expression Patterns, Gene Sets, Transformation, Visualisation
Added: 2019-11-12, Updated: 2019-11-12

L

LTMGSCA

LTMGSCA is a left truncated mixture Gaussian (LTMG) model-based single cell RNA-seq analysis pipeline that can accurately infer the modality and distribution of individual gene’s expression profile in scRNA-seq data, while decrease the impact from dropout and low expression value.

Publications: 1, Preprints: 1, Total citations: 46

Publications
"LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data"
DOI: 10.1093/nar/gkz655, Published: 2019-08-02, Citations: 46
Preprints
"LTMG: A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data"
DOI: 10.1101/430009, Citations: 0

Platform: R
Code: https://github.com/clwan/LTMGSCA
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Clustering, Differential Expression, Dimensionality Reduction, Modality, Transformation, Visualisation
Added: 2019-08-12, Updated: 2020-04-29

S

scBoolSeq

scRNA-Seq data binarisation and synthetic generation from Boolean dynamics

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

Preprints
"scBoolSeq: Linking scRNA-Seq Statistics and Boolean Dynamics"
DOI: 10.1101/2023.10.23.563518, Citations: 0

Platform: Python
Code: https://github.com/bnediction/scBoolSeq
starsN/A
forksN/A
last commitUnknown
License: BSD-3-Clause
Categories: Simulation, Transformation
Added: 2023-11-03, Updated: 2023-11-03

scPSD

A novel pre-processing method (scPSD) inspired by power spectral density analysis to extract important information from large-scale single-cell omics data and enhance the separation of cellular phenotypes

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

Publications
"Disentangling single-cell omics representation with a power spectral density-based feature extraction"
DOI: 10.1093/nar/gkac436, Published: 2022-05-25, Citations: 5
Preprints
"Disentangling single-cell omics representation with a power spectral density-based feature extraction"
DOI: 10.1101/2021.10.25.465657, Citations: 0

Platform: MATLAB/Python/R
Code: https://github.com/VafaeeLab/psdMAT
starsN/A
forksN/A
last commitUnknown
Categories: Transformation
Added: 2021-10-29, Updated: 2022-06-17

sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
Platform: R
Code: https://github.com/ChristophH/sctransform
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Differential Expression, Integration, Normalisation, Transformation, Visualisation
Added: 2018-07-27, Updated: 2018-07-27

T

transformGamPoi

transformGamPoi provides methods to stabilize the variance of single cell count data

Publications: 1, Preprints: 1, Total citations: 88

Publications
"Comparison of transformations for single-cell RNA-seq data"
DOI: 10.1038/s41592-023-01814-1, Published: 2023-04-10, Citations: 74
Preprints
"Transformation and Preprocessing of Single-Cell RNA-Seq Data"
DOI: 10.1101/2021.06.24.449781, Citations: 14

Platform: R
Code: https://github.com/const-ae/transformGamPoi
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Normalisation, Transformation
Added: 2021-07-02, Updated: 2023-05-12