Search Results - RepositoryStats

scanpy scverse

606

2.0k

bsd-3-clause

49

Single-cell analysis in Python. Scales to >1M cells.

python scanpy anndata scverse data-science bioinformatics visualize-data transcriptomics machine-learning

Created 2017-01-29

3,500 commits to main branch, last one a day 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

4,123 commits to main branch, last one 5 days ago

anndata scverse

155

588

bsd-3-clause

14

Annotated data.

scanpy anndata scverse data-science bioinformatics transcriptomics machine-learning

Created 2017-08-11

1,430 commits to main branch, last one 2 days ago

ehrapy theislab

20

244

apache-2.0

5

Electronic Health Record Analysis with Python.

ehr scverse electronic-health-record electronic-medical-record

Created 2021-06-11

1,773 commits to main branch, last one 3 days ago

muon scverse

31

222

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 about a month ago

rapids_singlecell scverse

22

157

mit

7

Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

gpu anndata scverse single-cell bioinformatics

Created 2021-05-05

498 commits to main branch, last one 2 days ago

pertpy scverse

22

147

mit

4

Perturbation Analysis in the scverse ecosystem.

scverse single-cell perturbation

Created 2021-06-23

975 commits to main branch, last one 10 days ago

infercnvpy icbi-lab

27

140

bsd-3-clause

4

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

cnv scverse single-cell

Created 2021-01-26

188 commits to main branch, last one 5 months ago

mudata scverse

17

79

bsd-3-clause

6

Multimodal Data (.h5mu) implementation for Python

muon mudata anndata scverse genomics multi-omics data-analysis multimodal-omics-analysis

Created 2021-08-04

597 commits to main branch, last one 2 months ago

scvi-tutorials scverse

25

47

bsd-3-clause

7

Notebooks used in scvi-tools tutorials

scverse tutorial scvi-tools

Created 2020-09-13

777 commits to main branch, last one 2 days ago

scdownstream nf-core

13

44

mit

179

A single cell transcriptomics pipeline for QC, integration and making the data presentable

scverse clustering integration single-cell quality-control dimensionality-reduction

Created 2024-06-11

480 commits to dev branch, last one 7 days ago

pytximport complextissue

1

30

gpl-3.0

1

Feature-rich Python implementation of the tximport package for gene count estimation.

rna deseq2 python anndata rna-seq scverse tximport bioinformatics

Created 2024-05-30

115 commits to main branch, last one 24 days 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

742 commits to main branch, last one 2 days ago