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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

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

SCP zhanghao-njmu

88

407

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

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

ceLLama CelVoxes

6

144

unknown

4

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

llm scanpy seurat rna-seq celltype single-cell large-language-models

Created 2024-06-16

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

cellxgene_VIP interactivereport

47

135

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

694 commits to master branch, last one 6 months ago

anndata2ri theislab

16

130

gpl-3.0

7

Convert between AnnData and SingleCellExperiment

rpy2 scanpy jupyter single-cell bioconductor

Created 2019-02-20

200 commits to main branch, last one 4 days ago

ncem theislab

13

104

bsd-3-clause

6

Learning cell communication from spatial graphs of cells

glm gnn cvae scanpy squidpy tensorflow cell-cell-interaction encoder-decoder-model cell-cell-communication

Created 2021-05-04

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

cirrocumulus lilab-bcb

16

76

bsd-3-clause

7

Bring your single-cell data to life

10x webgl scanpy seurat anndata spatial scrna-seq smartseq2 single-cell visualization bioinformatics transcriptomics data-visualization

Created 2019-10-04

2,110 commits to main branch, last one 3 months ago