Search Results - RepositoryStats

373

1.3k

bsd-3-clause

26

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

4,155 commits to main branch, last one a day ago

salmon COMBINE-lab

164

786

gpl-3.0

38

🐟 🍣 🍱 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 10 months ago

scRNA-seq_notes mdozmorov

151

660

mit

30

A list of scRNA-seq analysis tools

scrna-seq single-cell

Created 2018-08-30

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

cellxgene chanzuckerberg

127

657

mit

34

An interactive explorer for single-cell transcriptomics data

dataviz scrna-seq scientific visualization transcriptomics

Created 2017-10-03

1,577 commits to main branch, last one 4 months ago

harmony immunogenomics

101

545

other

25

Fast, sensitive and accurate integration of single-cell data with Harmony

r algorithm scrna-seq data-integration

Created 2018-06-12

318 commits to master branch, last one 2 months ago

SCP zhanghao-njmu

94

433

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 about a year ago

dynamo-release aristoteleo

59

432

bsd-3-clause

10

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

dynamo nasc-seq sci-fate scnt-seq cell-fate scrna-seq scslam-seq rna-jacobian rna-velocity vector-field rna-curvature rna-divergence rna-acceleration dynamical-systems potential-landscape differential-geometry

Created 2019-07-05

4,170 commits to master branch, last one about a month ago

scarches theislab

52

348

bsd-3-clause

12

Reference mapping for single-cell genomics

scrna-seq multiomics single-cell deep-learning batch-correction data-integration human-cell-atlas rna-seq-analysis single-cell-genomics multimodal-deep-learning

Created 2019-08-12

1,175 commits to master branch, last one 7 months ago

celltypist Teichlab

46

330

mit

8

A tool for semi-automatic cell type classification

python scrna-seq single-cell label-transfer machine-learning cell-type-classification

Created 2021-05-19

743 commits to main branch, last one about a month ago

scRNA-tools scRNA-tools

77

312

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

3,643 commits to main branch, last one 2 months ago

scRNAtoolVis junjunlab

30

309

other

3

Useful functions to make your scRNA-seq plot more cool!

yyds elegant scrna-seq visualization

Created 2022-06-23

115 commits to master branch, last one 12 days ago

MAESTRO liulab-dfci

78

279

gpl-3.0

12

Single-cell Transcriptome and Regulome Analysis Pipeline

scrna-seq scatac-seq epigenetics snakemake-workflows transcription-factors gene-regulatory-networks

Created 2019-07-16

614 commits to master branch, last one 3 years ago

scgen theislab

55

278

gpl-3.0

9

Single cell perturbation prediction

scrna-seq single-cell deep-learning bioinformatics transcriptomics generative-model single-cell-genomics

Created 2018-11-28

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

single-cell-papers-with-code genecell

70

275

unknown

12

Papers with code for single cell related papers

scrna-seq single-cell paper-with-code single-cell-omics scrna-seq-analysis reproducible-science single-cell-atac-seq reproducible-research

Created 2020-07-27

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

Tangram broadinstitute

51

268

bsd-3-clause

13

Spatial alignment of single cell transcriptomic data.

visium scrna-seq snrna-seq spatial-data gene-expression computational-biology

Created 2020-08-21

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

scCustomize samuel-marsh

24

237

gpl-3.0

2

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

3,101 commits to master branch, last one about a month ago

Palantir dpeerlab

53

233

gpl-2.0

11

Single cell trajectory detection

scrna-seq markov-chain diffusion-maps differentiation manifold-learning scrna-seq-analysis single-cell-genomics cell-fate-transitions trajectory-generation dimensionality-reduction

Created 2017-11-22

286 commits to master branch, last one 2 months ago

muon scverse

30

224

bsd-3-clause

14

muon is a multimodal omics Python framework

muon mudata scanpy anndata scverse cite-seq scrna-seq scatac-seq multi-omics multimodal-data multimodal-omics-analysis

Created 2020-02-03

586 commits to main branch, last one 3 months ago

splatter Oshlack

57

222

gpl-3.0

6

Simple simulation of single-cell RNA sequencing data

scrna-seq simulation bioconductor bioinformatics

Created 2016-10-04

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

pagoda2 kharchenkolab

47

220

unknown

16

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 11 months ago

conos kharchenkolab

39

203

gpl-3.0

12

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 11 months ago

souporcell wheaton5

46

174

mit

11

Clustering scRNAseq by genotypes

genomics scrnaseq scrna-seq bioinformatics scrna-seq-analysis computational-biology

Created 2019-03-16

228 commits to master branch, last one 5 months ago

STREAM pinellolab

48

173

agpl-3.0

16

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

python lineage scrna-seq scatac-seq singlecell trajectory visualization

Created 2018-04-12

471 commits to master branch, last one 3 years ago

kb_python pachterlab

23

159

bsd-2-clause

12

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

bustools kallisto kb-python scrna-seq single-cell-rna-seq rna-velocity-estimation

Created 2019-10-14

604 commits to master branch, last one 3 months ago

zellkonverter theislab

28

157

other

5

Conversion between scRNA-seq objects

r scrna-seq conversion bioconductor

Created 2020-06-08

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

cellxgene_VIP interactivereport

47

138

mit

6

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also pe...

svg scanpy seurat cellxgene scrna-seq cellxgene-vip visualization publication-quality-plots

Created 2020-05-06

697 commits to master branch, last one 15 hours ago

multinichenetr saeyslab

15

133

gpl-3.0

3

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

scrna-seq single-cell ligand-target ligand-receptor systems-biology single-cell-rna-seq cell-cell-interaction cell-cell-communication differential-expression intercellular-signaling intercellular-communication ligand-receptor-interaction

Created 2021-02-16

137 commits to main branch, last one 15 days ago

lamindb laminlabs

13

133

apache-2.0

2

A data framework for biology.

omics biology datalake lakehouse scrna-seq ontologies data-science bioinformatics data-engineering machine-learning

Created 2022-04-15

3,910 commits to main branch, last one 9 hours ago

iCellR rezakj

19

121

unknown

13

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptom...

3d umap icellr dropout cite-seq scrna-seq scvdj-seq clustering imputation pseudotime 10xgenomics normalization diffusion-maps intractive-graph batch-normalization clustering-algorithm singel-cell-sequencing cell-type-classification

Created 2018-12-11

84 commits to master branch, last one 6 months ago

ROGUE PaulingLiu

17

117

bsd-3-clause

4

Assessing the purity of single cell population

purity scrna-seq clustering quantification

Created 2019-09-27

51 commits to master branch, last one 4 years ago