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The Top 22 Python Bioinformatics Single Cell Open Source Projects

Open source projects categorized as Python Bioinformatics Single Cell
Categories > Data Processing > Bioinformatics
Categories > Single Cell
Awesome Single Cell ⭐ 2,784
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
most recent commit 3 months ago
Glue ⭐ 294
Graph-linked unified embedding for single-cell multi-omics data integration
most recent commit 5 months ago
Dance ⭐ 284
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
total releases 4most recent commit 3 months ago
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9most recent commit 7 months agopypi scgen} Downloads
Decoupler Py ⭐ 112
Python package to perform enrichment analysis from omics data.
dependent packages 3total releases 10most recent commit 3 months agopypi decoupler} Downloads
Sinto ⭐ 86
Tools for single-cell data processing
total releases 32most recent commit 7 months ago
Cell_blast ⭐ 74
A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
total releases 8most recent commit 9 months ago
Slat ⭐ 52
Spatial-Linked Alignment Tool
total releases 2most recent commit 4 months ago
Cell2cell ⭐ 44
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
most recent commit 5 months ago
Ngs ⭐ 30
Next-Gen Sequencing tools from the Horvath Lab
most recent commit a year ago
Cell2sentence Ft ⭐ 21
Cell2Sentence turns scRNA-seq data into text for LLM training.
most recent commit 7 months ago
Cshl Singlecell 2017 ⭐ 20
Single Cell Analysis course at Cold Spring Harbor Laboratory 2017
most recent commit 6 years ago
Crop Seq ⭐ 19
Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
most recent commit 6 years ago
Mdmcleaner ⭐ 13
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
total releases 5most recent commit a year ago
Rna Combine ⭐ 11
RNA-seq data comprehensive data analysis toolbox
most recent commit 2 years ago
Marcopolo ⭐ 9
MarcoPolo is a clustering-free approach to the exploration of bimodally expressed genes along with group information in single-cell RNA-seq data
total releases 12most recent commit a year ago
Trisicell ⭐ 9
Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data
total releases 25most recent commit 4 months ago
Cellcano ⭐ 8
Supervised cell type identification for scATAC-seq data
total releases 7most recent commit 8 months ago
Irescue ⭐ 8
A tool to quantify transposable elements expression in scRNA-seq
total releases 5most recent commit a year ago
Singlecellhaystack Py ⭐ 8
Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).
total releases 5most recent commit 3 months ago
Scphylo Tools ⭐ 5
a python toolkit for single-cell tumor phylogenetic analysis
total releases 5most recent commit 4 months ago
Genomap ⭐ 5
Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
total releases 24most recent commit 8 months ago
The 2 Most Depended On Python Bioinformatics Single Cell Open Source Projects
Decoupler Py ⭐ 112
Python package to perform enrichment analysis from omics data.
dependent packages 3total releases 10latest release August 31, 2023most recent commit 3 months agopypi decoupler} Downloads
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9latest release April 25, 2022most recent commit 7 months agopypi scgen} Downloads
The 10 Latest Releases In Python Bioinformatics Single Cell Open Source Projects
Dance ⭐ 284
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
total releases 4latest release December 04, 2023most recent commit 3 months ago
Sinto ⭐ 86
Tools for single-cell data processing
total releases 32latest release September 07, 2023most recent commit 7 months ago
Decoupler Py ⭐ 112
Python package to perform enrichment analysis from omics data.
dependent packages 3total releases 10latest release August 31, 2023most recent commit 3 months agopypi decoupler} Downloads
Scphylo Tools ⭐ 5
a python toolkit for single-cell tumor phylogenetic analysis
total releases 5latest release July 26, 2023most recent commit 4 months ago
Trisicell ⭐ 9
Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data
total releases 25latest release July 21, 2023most recent commit 4 months ago
Slat ⭐ 52
Spatial-Linked Alignment Tool
total releases 2latest release April 17, 2023most recent commit 4 months ago
Irescue ⭐ 8
A tool to quantify transposable elements expression in scRNA-seq
total releases 5latest release March 13, 2023most recent commit a year ago
Cell_blast ⭐ 74
A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
total releases 8latest release February 08, 2023most recent commit 9 months ago
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