Repositories list

• activelearning

  Public
  Active learning tools for fine-tuning ML models

  Python

  •

  MIT License

  •0•2•0•0•Updated Feb 4, 2025Feb 4, 2025

• nf-tenx

  Public
  All 10x Genomics processing pipelines rolled into one containerized pipelines

  bioinformaticspipeline

  Groovy

  •

  MIT License

  •1•7•4•2•Updated Feb 4, 2025Feb 4, 2025

• quilt-nf

  Public
  R

  •0•1•0•0•Updated Feb 4, 2025Feb 4, 2025

• ontology-annotation-network

  Public
  A rest-api to serve a neo4j database of supported ontology annotations.

  Java

  •

  Other

  •0•2•0•1•Updated Feb 3, 2025Feb 3, 2025

• LIRICAL

  Public
  LIkelihood Ratio Interpretation of Clinical AbnormaLities

  Java

  •

  Other

  •11•25•10•3•Updated Jan 31, 2025Jan 31, 2025

• STQ

  Public
  Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images

  spatial-transcriptomicsrna-velocityvisium+ 4xenomehe-stained-wsixengsortspecies-deconvolution

  Nextflow

  •

  MIT License

  •0•15•2•0•Updated Jan 31, 2025Jan 31, 2025

• DccXmlGenerator

  Public
  This is the Python version of the DCC XML file generator.

  Python

  •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

• biodownload

  Public
  BioDownload library

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•2•0•Updated Jan 27, 2025Jan 27, 2025

• jax-omeroutils

  Public
  A module and scripts for working with OMERO

  omeroomero-importimaging-solutions

  Python

  •

  GNU General Public License v2.0

  •3•6•4•1•Updated Jan 22, 2025Jan 22, 2025

• Cellos

  Public
  Python

  •

  MIT License

  •1•1•0•0•Updated Jan 15, 2025Jan 15, 2025

• geneweaver-boolean-algebra

  Public
  Python

  •

  Apache License 2.0

  •0•3•0•0•Updated Jan 15, 2025Jan 15, 2025

• geneweaver-tools

  Public
  Python

  •

  Apache License 2.0

  •0•2•0•0•Updated Jan 15, 2025Jan 15, 2025

• haplotype_reconstruction_qtl-nf

  Public
  R

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• cancer-cube-st-pilot-ffpe-ff

  Public
  Pilot Visium 10X experiment comparing FFPE and fresh frozen protocols

  Jupyter Notebook

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• FetchDCCResult

  Public template
  Python

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• geneweaver-legacy

  Public
  JavaScript

  •0•1•1•0•Updated Jan 8, 2025Jan 8, 2025

• hpo-web

  Public
  a web application to search and navigate the Human Phenotype Ontology (HPO)

  groovyhpograils3+ 1angular

  HTML

  •

  Other

  •12•13•5•9•Updated Jan 8, 2025Jan 8, 2025

• ontology-service

  Public
  A generic ontology term microservice

  Java

  •1•4•6•0•Updated Jan 7, 2025Jan 7, 2025

• geneweaver-docs

  Public
  Documentation site for the Geneweaver project.

  markdowngenomicsmkdocs+ 4documentation-sitefunctional-genomicsgenomic-data-sciencegeneweaver

  Apache License 2.0

  •0•4•4•1•Updated Jan 7, 2025Jan 7, 2025

• rit-imageanalysis-containers

  Public
  Making it easier for users to spin up a Singularity container with image analysis tools from a slurm-based cluster

  imaging-solutions

  Shell

  •

  MIT License

  •3•3•3•0•Updated Jan 6, 2025Jan 6, 2025

• cs-nf-pipelines

  Public
  The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines

  Nextflow

  •

  MIT License

  •10•20•0•0•Updated Jan 3, 2025Jan 3, 2025

• Images_Import_Scripts

  Public
  Python

  •0•0•0•0•Updated Jan 2, 2025Jan 2, 2025

• lama_workflow

  Public
  Repo with the inner workings for a container-based LAMA workflow.

  imaging-solutions

  Shell

  •

  MIT License

  •0•0•0•0•Updated Dec 31, 2024Dec 31, 2024

• CSNA

  Public
  The Center for Systems Neurogenetics of Addiction (CSNA)

  HTML

  •0•1•0•0•Updated Dec 30, 2024Dec 30, 2024

• Galaxy_Tools_CBA

  Public
  This is the Python and config files for the CBA tools deployed in Galaxy

  Python

  •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• imaging-applications-documentation

  Public
  Creative Commons Attribution 4.0 International

  •0•1•0•0•Updated Dec 13, 2024Dec 13, 2024

• geneweaver-client

  Public
  A client library for the integration and analysis of heterogeneous functional genomics data.

  genomicsanalyticsfunctional-genomics

  Python

  •

  Apache License 2.0

  •0•3•0•0•Updated Dec 11, 2024Dec 11, 2024

• geneweaver-api

  Public
  A system for the integration and analysis of heterogeneous functional genomics data.

  genomicsanalysisfunctional-genomics+ 1genomic-data-science

  Python

  •

  Apache License 2.0

  •0•5•0•0•Updated Dec 10, 2024Dec 10, 2024

• singularity-workshop-2023

  Public
  Other

  •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• KOMP_Images_ETL

  Public
  Python

  •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024