Search Results - RepositoryStats

seurat satijalab

918

2.3k

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 6 months ago

scvi-tools scverse

353

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

4,100 commits to main branch, last one 2 days ago

salmon COMBINE-lab

165

777

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 8 months ago

nichenetr saeyslab

117

489

unknown

14

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

495 commits to master branch, last one 2 months ago

squidpy scverse

82

441

bsd-3-clause

10

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

678 commits to main branch, last one 8 days ago

SCP zhanghao-njmu

85

395

gpl-3.0

8

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

dance OmicsML

36

351

bsd-2-clause

7

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

787 commits to main branch, last one 4 months ago

cellrank theislab

46

349

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

2,287 commits to main branch, last one about a month ago

monocle3 cole-trapnell-lab

102

342

other

21

This repository has no description...

single-cell-rna-seq

Created 2019-01-24

927 commits to master branch, last one 7 months ago

scRNA-tools scRNA-tools

77

309

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

3,631 commits to main branch, last one 22 days ago

MuSiC xuranw

94

233

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 8 months ago

scCustomize samuel-marsh

24

218

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 8 months ago

pagoda2 kharchenkolab

47

212

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 8 months ago

conos kharchenkolab

39

199

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 8 months ago

diffxpy theislab

23

193

bsd-3-clause

7

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

dittoSeq dtm2451

18

191

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 6 months ago

alevin-fry COMBINE-lab

15

169

bsd-3-clause

9

🐟 🔬🦀 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

807 commits to master branch, last one 4 months ago

numbat kharchenkolab

23

168

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

958 commits to main branch, last one 2 months ago

liana-py saezlab

21

167

gpl-3.0

3

LIANA+: an all-in-one framework for cell-cell communication

python spatial single-cell spatialomics ligand-receptor single-cell-rna-seq cell-cell-communication

Created 2022-09-22

810 commits to main branch, last one 2 months ago

SCpubr enblacar

13

158

gpl-3.0

6

Generate high quality, publication ready visualizations for single cell transcriptomics data.

r rstats seurat ggplot2 single-cell visualization data-visualization single-cell-rna-seq single-cell-genomics publication-quality-plots

Created 2021-12-21

734 commits to main branch, last one 3 months ago

tidyseurat stemangiola

12

157

unknown

9

Seurat meets tidyverse. The best of both worlds.

pca sct tsne umap dplyr purrr tidyr seurat tibble ggplot2 tidyverse single-cell transcripts normalization single-cell-rna-seq

Created 2020-08-23

414 commits to master branch, last one 4 months ago

scRNAseq_analysis_vignette quadbio

58

155

unknown

6

Tutorial for scRNA-seq data analysis beginners using R

tutorial bioinformatics single-cell-rna-seq single-cell-analysis

Created 2020-04-19

37 commits to master branch, last one 7 months ago

kb_python pachterlab

23

154

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 about a month ago

seurat-disk mojaveazure

49

152

gpl-3.0

14

Interfaces for HDF5-based Single Cell File Formats

hdf5-format single-cell-rna-seq single-cell-genomics

Created 2019-12-16

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

scCODA theislab

24

150

bsd-3-clause

9

A Bayesian model for compositional single-cell data analysis

tensorflow single-cell-rna-seq statistical-analysis compositional-changes

Created 2019-01-21

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

multinichenetr saeyslab

14

123

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

135 commits to main branch, last one 2 days ago

dynmethods dynverse

26

120

other

10

A collection of 50+ trajectory inference methods within a common interface 📥📤

single-cell-rna-seq single-cell-analysis trajectory-inference pseudotemporal-ordering bioinformatics-algorithms trajectory-inference-methods

Created 2017-11-14

1,315 commits to master branch, last one 11 months ago

SC3 hemberg-lab

55

119

gpl-3.0

11

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

human-cell-atlas single-cell-rna-seq bioconductor-package

Created 2016-01-28

363 commits to master branch, last one 4 years ago

scplotter pwwang

13

113

gpl-3.0

1

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

visualization single-cell-rna-seq single-cell-analysis single-cell-sequencing

Created 2024-09-03

37 commits to master branch, last one 15 days ago

scDRS martinjzhang

16

113

mit

2

Single-cell disease relevance score (scDRS)

gwas cell-state single-cell-rna-seq diseases-and-complex-traits within-cell-type-heterogeneity

Created 2020-07-10

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