Repositories list

• 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

• geneweaver-legacy

  Public
  JavaScript

  •0•1•1•1•Updated Dec 31, 2024Dec 31, 2024

• geneweaver-docs

  Public
  Documentation site for the Geneweaver project.

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

  Apache License 2.0

  •0•4•4•1•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

• DccXmlGenerator

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

  Python

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

• haplotype_reconstruction_qtl-nf

  Public
  R

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• ontology-service

  Public
  A generic ontology term microservice

  Java

  •1•3•7•0•Updated Dec 19, 2024Dec 19, 2024

• hpo-web

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

  groovyhpograils3+ 1angular

  HTML

  •

  Other

  •12•13•8•9•Updated Dec 19, 2024Dec 19, 2024

• geneweaver-boolean-algebra

  Public
  Python

  •

  Apache License 2.0

  •0•3•0•1•Updated Dec 18, 2024Dec 18, 2024

• quilt-nf

  Public
  R

  •0•1•0•0•Updated Dec 16, 2024Dec 16, 2024

• imaging-applications-documentation

  Public
  Creative Commons Attribution 4.0 International

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

• ontology-annotation-network

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

  Java

  •

  Other

  •0•2•0•0•Updated Dec 12, 2024Dec 12, 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

• 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•2•Updated Dec 9, 2024Dec 9, 2024

• activelearning

  Public
  Active learning tools for fine-tuning ML models

  Python

  •

  MIT License

  •0•2•0•0•Updated Dec 9, 2024Dec 9, 2024

• KOMP_Images_ETL

  Public
  Python

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

• intro_qupath_workshop

  Public
  Slides for Intro to QuPath workshop

  MIT License

  •1•1•0•0•Updated Nov 29, 2024Nov 29, 2024

• fiji_workshops

  Public
  Repository for Fiji workshop materials

  JavaScript

  •

  MIT License

  •5•0•0•0•Updated Nov 29, 2024Nov 29, 2024

• intro_cellprofiler_workshop

  Public
  Introduction slides for an Intro to CellProfiler workshop

  0•0•0•0•Updated Nov 29, 2024Nov 29, 2024

• intro-napari-workshop

  Public
  Intro to napari Workshop

  visualizationpythonnapari

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

  •2•1•1•0•Updated Nov 29, 2024Nov 29, 2024

• STQ

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

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

  Python

  •

  MIT License

  •0•15•2•0•Updated Nov 20, 2024Nov 20, 2024

• meta_mapper

  Public
  Map fields in existing metadata documents to those in new, standardized templates.

  Python

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• geneweaver-db

  Public
  The GeneWeaver database interaction code.

  sqlgenomicsfunctional-genomics+ 2genomic-data-sciencegeneweaver

  Python

  •

  Apache License 2.0

  •0•2•0•0•Updated Nov 6, 2024Nov 6, 2024

• ezomero

  Public
  A module with convenience functions for writing Python code that interacts with OMERO.

  omeroomero-serverimaging-solutions+ 2omero-apipython

  Python

  •

  GNU General Public License v2.0

  •13•39•3•1•Updated Oct 30, 2024Oct 30, 2024

• nf-tenx

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

  bioinformaticspipeline

  Groovy

  •

  MIT License

  •1•7•3•1•Updated Oct 24, 2024Oct 24, 2024

• omero-k8s-templates

  Public
  omeroimaging-solutions

  Dockerfile

  •

  GNU General Public License v2.0

  •1•1•0•0•Updated Oct 18, 2024Oct 18, 2024

• imaging_applications

  Public
  repository for Imaging Applications Github Page

  Lua

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024