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seurat satijalab

922

2.3k

other

76

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 7 months ago

scvi-tools scverse

366

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

4,133 commits to main branch, last one 22 hours ago

squidpy scverse

84

448

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

683 commits to main branch, last one 14 days ago

SCP zhanghao-njmu

88

410

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

cellrank theislab

47

354

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

2,288 commits to main branch, last one 11 days ago

scarches theislab

52

344

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 6 months ago

seurat-wrappers satijalab

131

312

gpl-3.0

11

Community-provided extensions to Seurat

community single-cell-analysis single-cell-genomics

Created 2019-04-24

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

scgen theislab

56

277

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

SnapATAC2 kaizhang

28

240

unknown

9

Single-cell epigenomics analysis tools

single-cell-genomics

Created 2021-12-04

503 commits to main branch, last one 11 days ago

scCustomize samuel-marsh

24

232

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

3,101 commits to master branch, last one 6 days ago

Palantir dpeerlab

52

230

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 25 days ago

SCpubr enblacar

13

164

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 4 months ago

seurat-disk mojaveazure

50

155

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

seurat-data satijalab

47

131

gpl-3.0

9

Dataset distribution for Seurat

datasets single-cell single-cell-genomics

Created 2019-05-29

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

azimuth satijalab

34

116

gpl-3.0

9

A Shiny web app for mapping datasets using Seurat v4

shiny-app single-cell-rna-seq single-cell-genomics

Created 2020-09-16

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

loupeR 10XGenomics

15

106

other

10

Convert Seurat objects to 10x Genomics Loupe files.

r-package 10xgenomics single-cell-genomics

Created 2023-08-23

30 commits to main branch, last one 13 days ago

swne yanwu2014

19

105

bsd-3-clause

5

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

bioinformatics data-visualization single-cell-rna-seq statistical-methods single-cell-analysis single-cell-atac-seq single-cell-genomics dimensionality-reduction nonnegative-matrix-factorization

Created 2018-01-03

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

scarf parashardhapola

12

98

bsd-3-clause

5

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Created 2020-05-07

1,024 commits to master branch, last one 8 days ago

cpa theislab

17

90

bsd-3-clause

5

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs...

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

Created 2021-10-15

344 commits to main branch, last one 4 months ago

scnym calico

12

73

apache-2.0

6

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

rna-seq single-cell semi-supervised adversarial-training single-cell-genomics

Created 2019-07-29

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

SCALEX jsxlei

18

73

bsd-3-clause

4

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

scalex single-cell deep-learning online-integration single-cell-genomics

Created 2021-03-09

94 commits to main branch, last one 5 days ago

cellDancer GuangyuWangLab2021

10

65

bsd-3-clause

0

Predict RNA velocity through deep learning

cell-fate rna-splicing rna-velocity transcriptomics single-cell-rna-seq single-cell-genomics rna-splicing-analysis rna-velocity-estimation

Created 2023-01-23

583 commits to main branch, last one about a year ago

single_cell_portal_core broadinstitute

26

63

bsd-3-clause

17

Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

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

Created 2016-03-17

12,528 commits to development branch, last one 7 days ago

sctour LiQian-XC

4

54

mit

3

A deep learning architecture for robust inference and accurate prediction of cellular dynamics

pseudotime latent-space vector-field deep-learning single-cell-genomics inference-and-prediction

Created 2022-01-03

94 commits to main branch, last one about a year ago

pyrovelocity pinellolab

5

46

agpl-3.0

8

𝒫robabilistic modeling of RNA velocity ⬱

pyro multiomics rna-splicing rna-velocity transcriptomics single-cell-rna-seq probabilistic-models single-cell-genomics deep-generative-model rna-splicing-analysis single-cell-multiomics cell-fate-determination rna-velocity-estimation probabilistic-programming developmental-trajectories

Created 2022-09-07

1,947 commits to main branch, last one 4 months ago

CREsted aertslab

2

28

other

7

CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

scverse scatac-seq deep-learning sequence-models regulatory-genomics single-cell-genomics

Created 2024-06-12

744 commits to main branch, last one a day ago