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    21 repositories

    • SimBu

      Public
      Simulate pseudo-bulk RNAseq samples from scRNAseq expression data
      R
      •
      GNU General Public License v3.0
      •1•17•5•2•Updated Jul 7, 2025Jul 7, 2025

    • deconvExplorer

      Public
      R
      •
      Other
      •1•4•5•2•Updated Jul 7, 2025Jul 7, 2025

    • spacedeconv

      Public
      A unified interface to spatial transcriptomics deconvolution tools
      R
      •
      GNU General Public License v3.0
      •8•41•6•3•Updated Jul 7, 2025Jul 7, 2025

    • omnideconv

      Public
      Unified access to several second-generation deconvolution methods
      HTML
      •
      GNU General Public License v3.0
      •15•73•20•3•Updated Jul 7, 2025Jul 7, 2025

    • immunedeconv

      Public
      A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods
      R
      •
      Other
      •101•497•33•4•Updated Jul 7, 2025Jul 7, 2025

    • DWLS

      Public
      DWLS R package patched and maintained to be used in the omnideconv installation
      R
      •3•1•0•0•Updated Jul 4, 2025Jul 4, 2025

    • methyldeconv_analysis

      Public
      R
      •0•0•0•0•Updated Jul 4, 2025Jul 4, 2025

    • methyldeconv

      Public
      Runs and compares different methylation based cell type deconvolution algorithms
      HTML
      •
      GNU General Public License v3.0
      •0•5•0•0•Updated Jun 27, 2025Jun 27, 2025

    • deconvBench

      Public
      Comparison of 2nd generation deconvolution methods implemented in omnideconv
      Jupyter Notebook
      •1•7•3•1•Updated Jun 24, 2025Jun 24, 2025

    • BayesPrism

      Public
      HTML
      •54•0•0•0•Updated Mar 25, 2025Mar 25, 2025

    • .github

      Public
      0•0•0•1•Updated Feb 20, 2025Feb 20, 2025

    • omnideconv.github.io

      Public
      CSS
      •0•2•0•1•Updated Feb 6, 2025Feb 6, 2025

    • AutoGeneS

      Public
      Jupyter Notebook
      •
      MIT License
      •8•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • scaden

      Public
      Deep Learning based cell composition analysis with Scaden.
      Python
      •
      MIT License
      •28•0•0•0•Updated Jun 7, 2024Jun 7, 2024

    • CDSeq

      Public
      CDSeq R package patched and maintained to be used in the omnideconv installation
      R
      •10•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • bseqsc

      Public
      Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
      R
      •16•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • MethylResolver

      Public
      Robust method for deconvolving bulk tissue methylation data using least trimmed squares (LTS) regression
      R
      •
      GNU General Public License v3.0
      •5•1•0•0•Updated Feb 16, 2024Feb 16, 2024

    • harmony

      Public
      Fast, sensitive and accurate integration of single-cell data with Harmony
      R
      •
      GNU General Public License v3.0
      •103•0•0•0•Updated Nov 17, 2022Nov 17, 2022

    • MuSiC

      Public
      Multi-subject Single Cell Deconvolution
      R
      •
      GNU General Public License v3.0
      •113•0•0•0•Updated Jul 28, 2022Jul 28, 2022

    • MOMF

      Public
      MOMF R package patched and maintained to be used in the omnideconv installation
      C++
      •
      GNU General Public License v3.0
      •8•0•0•0•Updated Nov 23, 2021Nov 23, 2021

    • SCDC

      Public
      SCDC R package patched and maintained to be used in the omnideconv installation
      R
      •11•0•0•0•Updated Jul 7, 2021Jul 7, 2021