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    49 repositories

    • smartid

      Public
      An R package for Scoring and Marker Selection Based on Modified TF-IDF
      R
      •
      Other
      •1•1•0•0•Updated Apr 22, 2026Apr 22, 2026

    • mastR

      Public
      An R package for automatically screening cell type signature in specific tissue/organ/cancer.
      R
      •
      Other
      •1•5•1•0•Updated Jan 26, 2026Jan 26, 2026

    • hoodscanR

      Public
      R
      •
      GNU General Public License v3.0
      •0•12•1•0•Updated Nov 12, 2025Nov 12, 2025

    • scDECAF

      Public
      Querying cellular states and programs by learning representations of gene sets
      scrna-seqgene-program
      scrna-seqgene-program
      R
      •3•16•1•0•Updated Nov 2, 2025Nov 2, 2025

    • scDECAF-reproducibility

      Public
      Code to reproduce figures for scDECAF manuscript
      Jupyter Notebook
      •0•0•0•0•Updated Nov 2, 2025Nov 2, 2025

    • standR

      Public
      Spatial transcriptomics analyses and decoding in R
      R
      •
      Other
      •6•24•8•0•Updated Oct 23, 2025Oct 23, 2025

    • singscore

      Public
      An R/Bioconductor package that implements a single-sample molecular phenotyping approach
      bioinformatics
      bioinformatics
      R
      •6•48•4•0•Updated Oct 13, 2025Oct 13, 2025

    • msImpute

      Public
      Methods for label-free mass spectrometry proteomics
      low-rank-approximationimputation-algorithmlabel-free-proteomics
      low-rank-approximationimputation-algorithmlabel-free-proteomics
      R
      •0•15•1•0•Updated Mar 23, 2025Mar 23, 2025

    • emtdata

      Public
      R
      •
      GNU General Public License v3.0
      •3•2•1•0•Updated Nov 21, 2024Nov 21, 2024

    • peptideprotonet_reproducibility

      Public
      Scripts and notebooks to reproduce figures for the peptideprotonet manuscript
      Jupyter Notebook
      •0•1•0•0•Updated Aug 18, 2024Aug 18, 2024

    • msigdb

      Public
      A R/Bioconductor ExperimentHub package to access gene expression signatures in the Molecular Signatures Database (MSigDB).
      R
      •
      Creative Commons Attribution 4.0 International
      •3•3•3•1•Updated Aug 8, 2024Aug 8, 2024

    • nf_modules

      Public
      Modules for scripting with nextflow
      Nextflow
      •0•0•4•0•Updated Jul 24, 2024Jul 24, 2024

    • SubcellularSpatialData

      Public
      This repository hosts a data package with annotated sub-cellular resolution spatial transcriptomics datasets.
      R
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Jul 11, 2024Jul 11, 2024

    • dcanr

      Public
      Differential co-expression/association network analysis
      R
      •3•7•0•0•Updated Jul 5, 2024Jul 5, 2024

    • SpatialLibrarySizePaper

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 9, 2024Apr 9, 2024

    • vissE

      Public
      An R/Bioconductor package to identify higher-order molecular phenotypes
      bioinformatics
      bioinformatics
      R
      •
      GNU General Public License v3.0
      •1•19•5•0•Updated Jan 15, 2024Jan 15, 2024

    • GeoMXAnalysisWorkflow

      Public
      GeoMX analysis workflow
      TeX
      •
      Other
      •3•8•8•0•Updated Nov 13, 2023Nov 13, 2023

    • msImpute-reproducibility

      Public
      Code to reproduce figures in msImpute manuscript and tutorials
      Jupyter Notebook
      •1•0•1•0•Updated May 28, 2023May 28, 2023

    • MultipleExperiment

      Public
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 2, 2023Mar 2, 2023

    • SingscoreAMLMutations

      Public
      R
      •4•1•1•0•Updated Oct 14, 2022Oct 14, 2022

    • maph

      Public
      a command line tool for analysing phosphoproteomics data
      R
      •0•0•0•0•Updated Mar 27, 2022Mar 27, 2022

    • BiocStickers

      Public
      Stickers for some Bioconductor packages - feel free to contribute and/or modify.
      R
      •112•0•0•0•Updated Mar 6, 2022Mar 6, 2022

    • SanJuan_etal_reproducibility

      Public
      Code to reproduce the results for San Juan et al. 2022
      HTML
      •0•0•0•0•Updated Feb 13, 2022Feb 13, 2022

    • peptide-protonet

      Public
      Embedding MS1 peptide features and identification transfer
      0•1•0•0•Updated Nov 4, 2021Nov 4, 2021

    • GenesetAnalysisWorkflow

      Public
      Dockerfile
      •
      GNU General Public License v3.0
      •1•4•0•0•Updated Oct 29, 2021Oct 29, 2021

    • Jacquelot_2021_reproducibility

      Public
      Source code and application note for ILC2 classifier developed in Jacquelot et al., 2021
      R
      •0•1•0•0•Updated Mar 15, 2021Mar 15, 2021

    • Db_Compare

      Public
      Compares the databases Reactome, KEGG, HPRD, WikiPathways and PhosphoSitePlus on their coverage of phospho/proteomic data.
      Python
      •0•2•0•0•Updated Feb 25, 2021Feb 25, 2021

    • mforoutan_tgfb_2017_tumours

      Public
      This repository contains Dockerfile for the following paper: A Transcriptional Signature for TGFβ-induced EMT in Cancer - Tumour analysis
      Dockerfile
      •0•0•0•0•Updated Aug 20, 2020Aug 20, 2020

    • mforoutan_tgfb_2017_celllines

      Public
      This repository contains Dockerfile for the following paper: A Transcriptional Signature for TGFβ-induced EMT in Cancer (cell-line analysis)
      Dockerfile
      •0•0•0•0•Updated Aug 20, 2020Aug 20, 2020

    • mforoutan_tgfb_paper_2016

      Public
      Docker file for TGFb paper
      Dockerfile
      •2•0•1•0•Updated Aug 20, 2020Aug 20, 2020
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