Repositories list

• spatiomic

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

  image-analysisspatial-proteomicsspatial-statistics+ 4

  image-analysisspatial-proteomicsspatial-statisticspathologymultiplexed-imagingscversepathoplex

  Python

  •

  Apache License 2.0

  •11 fork in complextissue/spatiomic•1919 stars in complextissue/spatiomic•11 issue in complextissue/spatiomic•11 pull request in complextissue/spatiomic•Updated Oct 26, 2026Oct 26, 2026

• 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

  •22 forks in complextissue/pytximport•4545 stars in complextissue/pytximport•00 issues in complextissue/pytximport•1111 pull requests in complextissue/pytximport•Updated Jul 10, 2026Jul 10, 2026

• phosphograph

  Public
  Python

  •

  GNU General Public License v3.0

  •00 forks in complextissue/phosphograph•11 star in complextissue/phosphograph•00 issues in complextissue/phosphograph•00 pull requests in complextissue/phosphograph•Updated May 20, 2026May 20, 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

  •00 forks in complextissue/pyclustree•2020 stars in complextissue/pyclustree•00 issues in complextissue/pyclustree•11 pull request in complextissue/pyclustree•Updated Mar 11, 2026Mar 11, 2026

• snakemake-bulk-rna-seq-workflow

  Public
  Snakemake workflow for bulk RNA sequencing with pytximport.

  Python

  •

  GNU General Public License v3.0

  •33 forks in complextissue/snakemake-bulk-rna-seq-workflow•99 stars in complextissue/snakemake-bulk-rna-seq-workflow•00 issues in complextissue/snakemake-bulk-rna-seq-workflow•00 pull requests in complextissue/snakemake-bulk-rna-seq-workflow•Updated Oct 24, 2025Oct 24, 2025

• PyDESeq2

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

  Python

  •

  MIT License

  •9393 forks in complextissue/PyDESeq2•00 stars in complextissue/PyDESeq2•00 issues in complextissue/PyDESeq2•00 pull requests in complextissue/PyDESeq2•Updated Sep 26, 2025Sep 26, 2025

• pasta

  Public
  Pattern Analysis of SpaTial omics datA

  TeX

  •44 forks in complextissue/pasta•00 stars in complextissue/pasta•00 issues in complextissue/pasta•00 pull requests in complextissue/pasta•Updated Mar 13, 2025Mar 13, 2025

• k-DBCV

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

  Python

  •

  MIT License

  •33 forks in complextissue/k-DBCV•00 stars in complextissue/k-DBCV•00 issues in complextissue/k-DBCV•00 pull requests in complextissue/k-DBCV•Updated Jan 23, 2025Jan 23, 2025

• multiSPAETI

  Public
  Implementation of MULTISPATI-PCA in Python

  Python

  •

  MIT License

  •11 fork in complextissue/multiSPAETI•00 stars in complextissue/multiSPAETI•00 issues in complextissue/multiSPAETI•00 pull requests in complextissue/multiSPAETI•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

  •446446 forks in complextissue/xpysom•00 stars in complextissue/xpysom•00 issues in complextissue/xpysom•00 pull requests in complextissue/xpysom•Updated Sep 20, 2023Sep 20, 2023

• .github

  Public
  00 forks in complextissue/.github•00 stars in complextissue/.github•00 issues in complextissue/.github•00 pull requests in complextissue/.github•Updated Feb 2, 2023Feb 2, 2023