Repositories list

• pytximport

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

  pythonbioinformaticsrna-seq+ 5

  pythonbioinformaticsrna-seqdeseq2rnatximportanndatascverse

  Python

  •

  GNU General Public License v3.0

  •2•43•0•1•Updated Mar 31, 2026Mar 31, 2026

• pyclustree

  Public
  A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.

  single-cellscverseclustree+ 1

  single-cellscverseclustreepyclustree

  Python

  •

  GNU General Public License v3.0

  •0•13•0•1•Updated Mar 11, 2026Mar 11, 2026

• spatiomic

  Public
  A Python package for unsupervised analysis of spatial (prote)omics data.

  image-analysisspatial-proteomicsspatial-statistics+ 4

  image-analysisspatial-proteomicsspatial-statisticspathologymultiplexed-imagingscversepathoplex

  Python

  •

  GNU General Public License v3.0

  •0•17•0•0•Updated Jan 5, 2026Jan 5, 2026

• snakemake-bulk-rna-seq-workflow

  Public
  Snakemake workflow for bulk RNA sequencing with pytximport.

  Python

  •

  GNU General Public License v3.0

  •3•7•0•0•Updated Oct 24, 2025Oct 24, 2025

• PyDESeq2

  Public
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

  Python

  •

  MIT License

  •80•0•0•0•Updated Sep 26, 2025Sep 26, 2025

• pasta

  Public
  Pattern Analysis of SpaTial omics datA

  TeX

  •4•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• k-DBCV

  Public
  High speed implementation of Density Based Cluster Validation (DBCV)

  Python

  •

  MIT License

  •3•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• multiSPAETI

  Public
  Implementation of MULTISPATI-PCA in Python

  Python

  •

  MIT License

  •1•0•0•0•Updated Nov 1, 2024Nov 1, 2024

• xpysom

  Public
  XPySom is a minimalistic implementation of batch Self Organizing Map algorithm

  Python

  •

  GNU General Public License v3.0

  •442•0•0•0•Updated Sep 20, 2023Sep 20, 2023

• .github

  Public
  0•0•0•0•Updated Feb 2, 2023Feb 2, 2023