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    13 repositories

    • pytximport

      Public
      Feature-rich Python implementation of the tximport package for gene count estimation.
      pythonbioinformaticsrna-seqdeseq2rnatximportanndatascverse
      Python
      •
      GNU General Public License v3.0
      •2•36•0•0•Updated Jul 24, 2025Jul 24, 2025

    • spatiomic

      Public
      A Python package for unsupervised analysis of spatial (prote)omics data.
      spatial-proteomicsspatial-statisticspathologyimage-analscversepathoplex
      Python
      •
      GNU General Public License v3.0
      •0•11•0•0•Updated Jul 18, 2025Jul 18, 2025

    • pyclustree

      Public
      A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.
      single-cellscverseclustreepyclustree
      Python
      •
      GNU General Public License v3.0
      •0•8•0•0•Updated Jun 8, 2025Jun 8, 2025

    • pertpy

      Public
      Perturbation Analysis in the scverse ecosystem.
      Python
      •
      MIT License
      •32•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • pasta

      Public
      Pattern Analysis of SpaTial omics datA
      TeX
      •3•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • decoupler-py

      Public
      Python package to perform enrichment analysis from omics data.
      Python
      •
      GNU General Public License v3.0
      •31•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • k-DBCV

      Public
      High speed implementation of Density Based Cluster Validation (DBCV)
      Python
      •
      MIT License
      •2•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • easySCFr

      Public
      R
      •5•1•0•0•Updated Nov 27, 2024Nov 27, 2024

    • PyDESeq2

      Public
      A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
      Python
      •
      MIT License
      •76•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • multiSPAETI

      Public
      Implementation of MULTISPATI-PCA in Python
      Python
      •
      MIT License
      •1•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • snakemake-bulk-rna-seq-workflow

      Public
      Snakemake workflow for bulk RNA sequencing with pytximport.
      Python
      •
      GNU General Public License v3.0
      •2•5•0•0•Updated Sep 30, 2024Sep 30, 2024

    • xpysom

      Public
      XPySom is a minimalistic implementation of batch Self Organizing Map algorithm
      Python
      •
      GNU General Public License v3.0
      •438•0•0•0•Updated Sep 20, 2023Sep 20, 2023

    • .github

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