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seurat satijalab

889

2.2k

other

74

R toolkit for single cell genomics

cran human-cell-atlas single-cell-rna-seq single-cell-genomics

Created 2015-05-20

8,541 commits to master branch, last one 21 days ago

scvi-tools scverse

342

1.1k

bsd-3-clause

28

Deep probabilistic analysis of single-cell and spatial omics data

scverse cite-seq scrna-seq deep-learning human-cell-atlas variational-bayes single-cell-rna-seq single-cell-genomics deep-generative-model variational-autoencoder

Created 2017-09-06

3,993 commits to main branch, last one 2 days ago

salmon COMBINE-lab

160

739

gpl-3.0

39

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

10x rnaseq salmon rna-seq sailfish scrna-seq c-plus-plus single-cell quasi-mapping transcriptome bioinformatics quantification gene-expression selective-alignment single-cell-rna-seq rna-seq-quantification

Created 2015-03-19

1,907 commits to master branch, last one 2 months ago

nichenetr saeyslab

113

441

unknown

15

NicheNet: predict active ligand-target links between interacting cells

rna-seq ligand-target gene-expression ligand-receptor data-integration network-inference single-cell-omics single-cell-rna-seq cell-cell-communication intercellular-communication

Created 2018-02-05

465 commits to master branch, last one a day ago

squidpy scverse

71

398

bsd-3-clause

9

Spatial Single Cell Analysis in Python

squidpy image-analysis spatial-analysis data-visualization single-cell-rna-seq single-cell-genomics spatial-transcriptomics

Created 2020-08-21

626 commits to main branch, last one 4 days ago

dance OmicsML

30

328

bsd-2-clause

6

DANCE: a deep learning library and benchmark platform for single-cell analysis

dance python benchmark single-cell data-science deep-learning multimodality bioinformatics machine-learning single-cell-rna-seq computational-biology graph-neural-networks spatial-transcriptomics single-cell-rna-sequencing

Created 2022-06-07

437 commits to main branch, last one 19 days ago

monocle3 cole-trapnell-lab

95

312

other

21

This repository has no description...

single-cell-rna-seq

Created 2019-01-24

927 commits to master branch, last one about a month ago

SCP zhanghao-njmu

66

312

gpl-3.0

7

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

scanpy seurat anndata scrna-seq shiny-app shinyapps scatac-seq shiny-apps single-cell scrna-pipeline seurat-objects single-cell-omics scrna-seq-analysis single-cell-rna-seq single-cell-analysis single-cell-atac-seq single-cell-genomics single-cell-pipeline single-cell-sequencing

Created 2022-03-30

308 commits to main branch, last one 6 months ago

cellrank theislab

38

305

bsd-3-clause

8

CellRank: dynamics from multi-view single-cell data

genetics data-science rna-velocity markov-chains bioinformatics machine-learning manifold-learning single-cell-rna-seq single-cell-genomics cell-fate-transitions trajectory-generation cell-fate-determination fuzzy-clustering-analyses

Created 2020-03-12

2,276 commits to main branch, last one about a month ago

scRNA-tools scRNA-tools

75

296

mit

21

Table of software for the analysis of single-cell RNA-seq data.

tools rna-seq database software scrna-seq single-cell single-cell-rna-seq

Created 2016-09-09

3,602 commits to main branch, last one 25 days ago

MuSiC xuranw

78

217

gpl-3.0

5

Multi-subject Single Cell Deconvolution

single-cell-rna-seq statistical-genetics

Created 2018-04-08

147 commits to master branch, last one 2 months ago

pagoda2 kharchenkolab

46

192

unknown

18

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

scrna-seq single-cell transcriptomics single-cell-rna-seq

Created 2017-04-25

1,483 commits to main branch, last one 3 months ago

conos kharchenkolab

38

189

gpl-3.0

13

R package for the joint analysis of multiple single-cell RNA-seq datasets

scrna-seq batch-correction single-cell-rna-seq

Created 2018-07-21

1,108 commits to main branch, last one 3 months ago

scCustomize samuel-marsh

19

179

gpl-3.0

3

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

seurat ggplot2 scrna-seq single-cell customization visualization single-cell-rna-seq single-cell-genomics

Created 2021-09-29

2,374 commits to master branch, last one 3 months ago

dittoSeq dtm2451

17

176

mit

5

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

rna-seq color-blind single-cell visualization color-blindness single-cell-rna-seq

Created 2019-02-18

828 commits to devel branch, last one about a month ago

diffxpy theislab

23

175

bsd-3-clause

6

Differential expression analysis for single-cell RNA-seq data.

tensorflow bioinformatics transcriptomics gene-set-enrichment single-cell-rna-seq differential-expression

Created 2018-07-02

478 commits to master branch, last one about a year ago

numbat kharchenkolab

22

156

other

9

Haplotype-aware CNV analysis from single-cell RNA-seq

phylogeny single-cell cnv-detection cancer-genomics lineage-tracing single-cell-rna-seq single-cell-analysis spatial-transcriptomics

Created 2021-05-25

942 commits to main branch, last one 28 days ago

alevin-fry COMBINE-lab

15

153

bsd-3-clause

7

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

10x rust rna-seq single-cell quantification transcriptomics single-cell-rna-seq

Created 2020-07-15

800 commits to master branch, last one 2 months ago