Repositories list

• flexynesis

  Public
  A deep-learning based multi-modal data integration suite that aims to achieve synesis in a flexible manner

  Python

  •

  Other

  •32•103•10•0•Updated Mar 31, 2026Mar 31, 2026

• dummy-spatialdata

  Public
  A package for creating dummy spatialdata objects for testing purposes.

  Python

  •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

• ImageArray

  Public
  R

  •

  Other

  •2•5•3•0•Updated Mar 27, 2026Mar 27, 2026

• pycacher

  Public
  Python

  •

  Other

  •0•0•0•0•Updated Mar 23, 2026Mar 23, 2026

• RSimpleITK

  Public
  R Installer for SimpleITK with Elastix

  Shell

  •0•0•0•0•Updated Mar 23, 2026Mar 23, 2026

• cacheR

  Public
  R

  •

  Other

  •0•1•1•0•Updated Mar 20, 2026Mar 20, 2026

• VoltRon

  Public
  Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration

  R

  •

  Other

  •21•118•1•1•Updated Mar 13, 2026Mar 13, 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

• rstudio

  Public
  RStudio is an integrated development environment (IDE) for R

  Java

  •

  Other

  •1.2k•0•0•0•Updated Feb 28, 2026Feb 28, 2026

• VoltRonStore

  Public
  On-Disk support and dependancies for VoltRon

  Other

  •1•0•0•0•Updated Feb 27, 2026Feb 27, 2026

• CompassDock

  Public
  Official Implementation of CompassDock

  drug-discoverymolecular-biologyprotein-ligand-interactions+ 3

  drug-discoverymolecular-biologyprotein-ligand-interactionsmolecular-dockingdrug-target-interactionsbinding-affinity

  Python

  •

  Other

  •3•21•0•0•Updated Feb 13, 2026Feb 13, 2026

• rcas-web

  Public
  Web interface for RCAS

  JavaScript

  •

  GNU Affero General Public License v3.0

  •0•1•0•0•Updated Feb 9, 2026Feb 9, 2026

• pigx_rnaseq

  Public
  Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline

  snakemakepipelinernaseq+ 2

  snakemakepipelinernaseqguixreproducibility

  Python

  •

  GNU General Public License v3.0

  •12•21•23•0•Updated Jan 30, 2026Jan 30, 2026

• OMERarr

  Public
  An R package for reading, writing and validating OME-Zarr (meta)data (based on ome-zarr-models.py)

  R

  •0•0•6•0•Updated Jan 30, 2026Jan 30, 2026

• teampulse

  Public
  team Pulse app

  HTML

  •0•0•0•0•Updated Jan 26, 2026Jan 26, 2026

• HDF5DataFrame

  Public
  R

  •

  Other

  •1•1•0•0•Updated Jan 20, 2026Jan 20, 2026

• collab_barleben_kolesnichenko_colitis

  Public
  Collaboration project with Luisa Barleben Kolesnichenko Lab - Acute Colitis in Mice

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 16, 2026Jan 16, 2026

• BPCells

  Public
  Scaling Single Cell Analysis to Millions of Cells

  C++

  •

  Other

  •31•0•0•0•Updated Jan 13, 2026Jan 13, 2026

• VoltRon_manuscript

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 4, 2026Jan 4, 2026

• causal_reasoning

  Public
  A collection of tools, which, when given a readout of a perturbation experiment, runs tools such as CARNIVAL/causalR to infer the causal factors that leads to t…

  R

  •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

• ZarrArray

  Public
  Zarr backend for DelayedArray objects

  R

  •0•2•3•0•Updated Dec 2, 2025Dec 2, 2025

• PocketVina

  Public
  GPU-accelerated protein-ligand docking with automated pocket detection, exploring through multi-pocket conditioning. Official Implementation of PocketVina

  protein-ligand-dockingdrug-discoverymolecular-biology+ 8

  protein-ligand-dockingdrug-discoverymolecular-biologyprotein-ligand-interactionsprotein-ligand-binding-affinitymolecular-dockingautodock-vinaautodock-gpup2rankquickvina+ 1

  C++

  •

  MIT License

  •10•71•2•1•Updated Nov 22, 2025Nov 22, 2025

• pigx_bsseq

  Public
  bisulfite sequencing pipeline from fastq to methylation reports

  bioinformaticssnakemakepipeline+ 2

  bioinformaticssnakemakepipelineguixreproducibility

  Python

  •

  GNU General Public License v3.0

  •4•13•47•1•Updated Nov 9, 2025Nov 9, 2025

• pigx-common

  Public
  Common infrastructure used by all PiGx pipelines

  Python

  •

  GNU General Public License v3.0

  •1•0•2•3•Updated Nov 9, 2025Nov 9, 2025

• anglemania

  Public
  Improved feature extraction for scRNA-seq dataset integration.

  R

  •

  GNU General Public License v3.0

  •0•4•5•0•Updated Oct 23, 2025Oct 23, 2025

• medLLMbenchmark

  Public
  Jupyter Notebook

  •

  MIT License

  •6•8•0•0•Updated Oct 21, 2025Oct 21, 2025

• protEncode

  Public
  Repository relating to the pipeline on using attention-weighted PLMs.

  Python

  •

  Creative Commons Zero v1.0 Universal

  •0•0•1•0•Updated Oct 21, 2025Oct 21, 2025

• protEncode-analysis

  Public
  Analysis scripts and demonstrations to accompany the protEncode package and related work.

  Jupyter Notebook

  •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025