scverse

There are 1 repository under scverse topic.

• scanpy

  scverse / scanpy

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

  machine-learningdata-sciencevisualize-datatranscriptomicsbioinformaticsscanpyanndatapythonscverse
  Language:Python 1837

• scverse / scvi-tools

  Deep probabilistic analysis of single-cell and spatial omics data

  scrna-seqvariational-bayesvariational-autoencodercite-seqsingle-cell-genomicssingle-cell-rna-seqdeep-generative-modelhuman-cell-atlasscversedeep-learning
  Language:Python 1178

• scverse / anndata

  Annotated data.

  scanpydata-sciencetranscriptomicsbioinformaticsmachine-learningscverseanndata
  Language:Python 544

• scverse / muon

  muon is a multimodal omics Python framework

  multimodal-datamultimodal-omics-analysismulti-omicsanndatascanpymudatamuonscrna-seqscatac-seqcite-seqscverse
  Language:Python 207

• theislab / ehrapy

  Electronic Health Record Analysis with Python.

  ehrelectronic-health-recordelectronic-medical-recordscverse
  Language:Python 135

• icbi-lab / infercnvpy

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

  cnvsingle-cellscverse
  Language:Python 128
• rapids_singlecell

  scverse / rapids_singlecell

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

  gpusingle-cellanndatabioinformaticsscverse
  Language:Python 123

• scverse / pertpy

  Perturbation Analysis in the scverse ecosystem.

  scversesingle-cellperturbation
  Language:Python 118

• scverse / mudata

  Multimodal Data (.h5mu) implementation for Python

  data-analysisgenomicsmulti-omicsmultimodal-omics-analysisanndatamudatamuonscverse
  Language:Python 72

• scverse / scvi-tutorials

  Notebooks used in scvi-tools tutorials

  scversetutorialscvi-tools
  Language:Jupyter Notebook 43

• scverse / Muon.jl

  Muon for Julia

  omicsmulti-omicssingle-cellmuonanndatamudatascversejulia
  Language:Julia 25

• nf-core / scdownstream

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

  clusteringdimensionality-reductionintegrationquality-controlscversesingle-cell
  Language:Nextflow 18

• scverse / muon-tutorials

  Tutorials for multimodal omics data analysis

  multi-omicssingle-cellmudatamuonscverse
  Language:Jupyter Notebook 11

• metaspace2020 / metaspace-converter

  Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData

  anndatametaspacepythonscversespatialdata
  Language:Python 8

• scverse / governance

  Governance docs for scverse

  governancescverse
  6

• vjcitn / scviR

  experimental interface between R and scvi-tools

  bioconductorcite-seqscverse
  Language:R 6

• gtca / chame

  Chromatin analysis module

  atac-seqchromatingenomemultiomerangesscatac-seqscverse
  Language:Python 4

• complextissue / pytximport

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

  anndatabioinformaticsdeseq2pythonrnarna-seqscversetximport
  Language:Python 3

• cantinilab / GRnnData

  Awesome GRN enhanced AnnData toolkit

  anndatagene-regulatory-networkrna-seqscversesingle-cellutils
  Language:Jupyter Notebook 1

• scverse / muon-site

  Muon website

  scversemuonmudata
  Language:JavaScript 1

• YosefLab / treedata

  anndata with trees

  anndatabioinformaticsdata-sciencelineage-tracingscanpyscverse
  Language:Python 1

• YosefLab / pycea

  scverse lineage tracing analysis toolkit

  bioinformaticslineage-tracingscanpyscversetreedata
  Language:Python