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    133 repositories

    • pigx_bsseq

      Public
      bisulfite sequencing pipeline from fastq to methylation reports
      bioinformaticssnakemakepipeline
      bioinformaticssnakemakepipelineguixreproducibility
      Python
      •
      GNU General Public License v3.0
      •4•13•48•0•Updated Jun 25, 2026Jun 25, 2026

    • pyanglemania

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 23, 2026Jun 23, 2026

    • atlas_tissue_representation

      Public
      Code and reproduction for the tissue-supervised VAE bulk RNA-seq manuscript
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • flexynesis

      Public
      A deep-learning based multi-modal data integration suite that aims to achieve synesis in a flexible manner
      Python
      •
      Other
      •35•109•12•0•Updated Jun 19, 2026Jun 19, 2026

    • pigx

      Public
      Pipelines in genomics
      snakemakegenomicsrnaseq
      snakemakegenomicsrnaseqguixdropseqbisulfite-sequencingchipseq
      HTML
      •
      GNU General Public License v3.0
      •7•23•9•0•Updated Jun 17, 2026Jun 17, 2026

    • ECGage

      Public
      HTML
      •0•0•0•0•Updated Jun 8, 2026Jun 8, 2026

    • flexynesis-guide

      Public
      Getting started with Flexynesis with help from Claude Code
      0•0•0•0•Updated Jun 5, 2026Jun 5, 2026

    • dummy-spatialdata

      Public
      Generate dummy spatialdata objects
      Python
      •0•3•1•0•Updated Jun 4, 2026Jun 4, 2026

    • compgen_course_2025_module3

      Public
      Compgen Course 2025, Module 3 Course Material, Multi-omics integration using deep learning
      Jupyter Notebook
      •31•64•0•0•Updated Jun 3, 2026Jun 3, 2026

    • ImageArray

      Public
      a framework for on-disk and in-memory image arrays
      R
      •
      Other
      •3•6•5•2•Updated May 30, 2026May 30, 2026

    • pigx_rnaseq

      Public
      Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
      snakemakepipelinernaseq
      snakemakepipelinernaseqguixreproducibility
      Python
      •
      GNU General Public License v3.0
      •13•21•23•0•Updated May 29, 2026May 29, 2026

    • swineherd

      Public
      Let the Shepherd herd Guix System containers
      TeX
      •
      GNU General Public License v3.0
      •1•30•1•0•Updated May 24, 2026May 24, 2026

    • pigx-common

      Public
      Common infrastructure used by all PiGx pipelines
      Python
      •
      GNU General Public License v3.0
      •1•0•1•2•Updated May 21, 2026May 21, 2026

    • pigx_chipseq

      Public
      Pipeline for Analysis of ChIP-Seq data
      snakemakepipelineguix
      snakemakepipelineguixreproducibilitychipseq
      Python
      •
      GNU General Public License v3.0
      •10•10•68•1•Updated May 20, 2026May 20, 2026

    • ECG_age

      Public
      Python
      •0•0•0•0•Updated May 20, 2026May 20, 2026

    • Course_AgenticDataAnalysis

      Public
      Python
      •0•2•0•0•Updated May 19, 2026May 19, 2026

    • neuroblastoma_gene_sets

      Public
      A repository for documentation and storage of neuroblastoma related gene sets
      Python
      •0•0•0•0•Updated May 18, 2026May 18, 2026

    • cacheR

      Public
      R
      •
      Other
      •0•1•0•0•Updated May 18, 2026May 18, 2026

    • rstudio

      Public
      RStudio is an integrated development environment (IDE) for R
      Java
      •
      Other
      •1.2k•0•0•0•Updated May 16, 2026May 16, 2026

    • RSimpleITK

      Public
      R Installer for SimpleITK with Elastix
      Shell
      •0•0•0•0•Updated May 13, 2026May 13, 2026

    • VoltRon

      Public
      Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
      R
      •
      Other
      •21•123•2•1•Updated Apr 28, 2026Apr 28, 2026

    • VoltRonStore

      Public
      On-Disk support and dependancies for VoltRon
      Other
      •1•0•0•0•Updated Apr 27, 2026Apr 27, 2026

    • ZarrDataFrame

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Apr 27, 2026Apr 27, 2026

    • pycacheR

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Apr 15, 2026Apr 15, 2026

    • OMERarr

      Public
      An R package for reading, writing and validating OME-Zarr (meta)data (based on ome-zarr-models.py)
      R
      •1•0•6•0•Updated Apr 10, 2026Apr 10, 2026

    • protEncode

      Public
      Repository relating to the pipeline on using attention-weighted PLMs.
      Python
      •
      Creative Commons Zero v1.0 Universal
      •0•1•1•0•Updated Apr 6, 2026Apr 6, 2026

    • SimpleITKRInstaller

      Public
      Remotes based SimpleITK R installer.
      R
      •11•0•0•0•Updated Mar 12, 2026Mar 12, 2026

    • bimsbbioinfo.r-universe.dev

      Public
      R-universe BIMSBbioinfo
      0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

    • Course_SystemsBiology

      Public
      JavaScript
      •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

    • CompassDock

      Public
      Official Implementation of CompassDock
      drug-discoverymolecular-biologyprotein-ligand-interactions
      drug-discoverymolecular-biologyprotein-ligand-interactionsmolecular-dockingdrug-target-interactionsbinding-affinity
      Python
      •
      Other
      •3•21•0•0•Updated Feb 13, 2026Feb 13, 2026
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