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    54 repositories

    • mev-backend

      Public
      RESTful API for WebMEV
      Python
      •
      MIT License
      •3•2•6•5•Updated Sep 13, 2024Sep 13, 2024

    • mev-spatialge-sthet

      Public
      Global spatial autocorrelation statistics on gene expression
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • mev-spatialge-stgradient

      Public
      Integration of stGradient tools from spatialGE into WebMeV
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • mev-frontend

      Public
      The front-end Angular 12 application for the MEV web application
      TypeScript
      •
      MIT License
      •0•3•6•0•Updated Sep 5, 2024Sep 5, 2024

    • mev-limma-voom

      Public
      WebMEV-compatible operation for running limma+voom for RNA-seq studies
      R
      •0•0•0•0•Updated Aug 26, 2024Aug 26, 2024

    • mev-edgeR

      Public
      Implementation of Bioconductor's edgeR for basic differential gene expression analysis
      R
      •0•0•0•0•Updated Aug 26, 2024Aug 26, 2024

    • deseq2

      Public
      WebMEV-compatible differential expression analysis based on DESeq2
      R
      •0•0•0•0•Updated Aug 26, 2024Aug 26, 2024

    • mev-spatialge-normalize

      Public
      Workflow for normalization of spatial count data.
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-spatialge-stclust

      Public
      Implementation of spatialGE's STclust algorithm for WebMeV.
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-sctk-importcellranger

      Public
      A tools for converting 10x sparse data into a WebMeV compatible TSV.
      R
      •
      MIT License
      •0•0•1•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-sctk-decontx

      Public
      An implementation of decontX for single cell vis SCTK for WebMeV
      R
      •
      MIT License
      •0•1•0•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-snf

      Public
      WebMeV-compatible implementation of the Similarity Network Fusion (SNF) algorithm
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-topgo

      Public
      TopGO analysis of differential expression results.
      R
      •
      MIT License
      •0•2•0•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-wgcna

      Public
      WGCNA (weighted gene correlation network analysis) for count data analysis
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-fgsea

      Public
      MEV-compatible implementation of the fgsea Bioconductor package
      R
      •0•0•1•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-lrt

      Public
      DESeq2 implementation of likelihood ratio test
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-combatseq

      Public
      WebMeV tool for executing CombatSeq adjustment
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • mev-normalize

      Public
      R
      •0•0•1•0•Updated Aug 22, 2024Aug 22, 2024

    • dummy-dge

      Public
      R
      •0•0•0•0•Updated Aug 20, 2024Aug 20, 2024

    • test-ecs

      Public
      Testing repository for ECS-based WebMeV jobs. Runs a basic PCA
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

    • mev-spotlight

      Public
      Pre-trained spotlight models for running on WebMeV.
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • mev-spatialge-stenrich

      Public
      Detection of gene sets with spatial aggregation patterns.
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • base-spatialge-docker

      Public
      Build instructions for docker container of spatialGE.
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

    • mev-hcl

      Public
      WebMeV-compatible tool for hierarchical clustering. Uses a Cromwell job runner.
      Python
      •0•0•0•0•Updated Jul 10, 2024Jul 10, 2024

    • tutorials

      Public
      Static site for WebMeV tutorials and other materials
      HCL
      •
      MIT License
      •0•0•0•0•Updated Jul 3, 2024Jul 3, 2024

    • mev-sctk-doubletfinder

      Public
      Multiplet QC with DoubletFinder.
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 3, 2024Jul 3, 2024

    • mev-sctk-mast

      Public
      Implementation of SCTK's MAST wrapper for differential gene expression for WebMeV.
      R
      •0•1•0•0•Updated Jun 28, 2024Jun 28, 2024

    • mev-sctk-singler

      Public
      SCTK's SingleR auto cell typing implementation.
      R
      •
      MIT License
      •0•0•0•0•Updated Jun 28, 2024Jun 28, 2024

    • mev-10x-import

      Public
      Utility for creating a flat matrix from the sparse, matrix-matrix format distributed by 10x Genomics
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 12, 2024Jun 12, 2024

    • mev-panda

      Public
      WebMeV implementation of NetZoo's PANDA algorithm for network analysis.
      Python
      •
      MIT License
      •0•0•1•0•Updated Apr 2, 2024Apr 2, 2024