PyRank
  • Insights
  • PyPI
  • GitHub
  • Search
  • Compare
  • Advisories
  • Ecosystem
  • About

Scrna Seq Python Packages

Python packages with the GitHub topic scrna-seq. Sorted by relevance, with stars and monthly downloads.
scverse
scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

94K 2K 450
scverse
muon

muon is a multimodal omics Python framework

29K 267 35
Teichlab
celltypist

A tool for semi-automatic cell type classification

16K 478 59
dpeerlab
palantir

Single cell trajectory detection

6K 310 61
Ekin-Kahraman
rustscenic

Rust and PyO3 implementation of SCENIC-style single-cell regulatory-network analysis. GRN, AUCell, topics, cisTarget, peak calling, cell QC, enhancer-gene links, and eRegulon assembly in one pip install.

5K 11 2
lilab-bcb
cirrocumulus

Bring your single-cell data to life

5K 97 17
JonathanShor
doubletdetection

Doublet detection in single-cell RNA-seq data.

4K 98 22
aristoteleo
dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

3K 494 60
pachterlab
kb-python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

3K 188 30
theislab
scarches

Reference mapping for single-cell genomics

3K 404 70
chanzuckerberg
cellxgene

Web application for exploration of large scale scRNA-seq datasets

2K 766 150
YosefLab
scvi

Deep probabilistic analysis of single-cell and spatial omics data

2K 2K 450
broadinstitute
tangram-sc

Spatial alignment of single cell transcriptomic data.

2K 365 64
parashardhapola
scarf

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.

2K 116 15
eleozzr
desc

Deep Embedding for Single-cell Clustering

2K 89 25
quadbio
cellmapper

k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.

2K 14 4
cbg-ethz
scdef

Deep exponential families for single-cell data.

1K 20 1
scDiffEq
larry-dataset

Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning

1K 4 1
potulabe
symphonypy

Port of symphony algorithm of single-cell reference atlas mapping to Python

1K 34 3
Novartis
cellxgene-gateway

Cellxgene Gateway

1K 68 41
bodegalab
irescue

Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq

1K 22 3
theislab
scgen

Single cell perturbation prediction

932 343 69
quadbio
scembed

Run embedding comparisons for single-cell data

860 5 1
XingyanLiu
came

cell-type assignment and gene module extraction of scRNA-seq

791 13 8
    • Data from PyPI, GitHub, ClickHouse, and BigQuery