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    42 repositories

    • infercnvpy

      Public
      Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
      single-cellcnvscverse
      single-cellcnvscverse
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •32•189•15•3•Updated Apr 27, 2026Apr 27, 2026

    • atlas_protocol

      Public
      A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022).
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •6•9•5•3•Updated Apr 27, 2026Apr 27, 2026

    • hairy_cell_leukemia

      Public
      Single-cell analysis of Hairy Cell Leukemia samples published in Bohn et al.
      Jupyter Notebook
      •0•0•0•0•Updated Apr 27, 2026Apr 27, 2026

    • diabetes_microbe

      Public
      Escherichia-Shigella Expansion and metabolite dysregulation in type 3c diabetes: linking microbiome alterations to exocrine pancreatic insufficiency
      HTML
      •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

    • icbi-lab.github.io

      Public
      For now, redirect to ICBI website.
      HTML
      •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

    • minigenie

      Public
      Python
      •0•0•0•0•Updated Dec 22, 2025Dec 22, 2025

    • mio

      Public
      HTML
      •1•0•0•2•Updated Oct 1, 2025Oct 1, 2025

    • crc-atlas

      Public
      Single-cell Colorectal Cancer Atlas with 4.27M cells
      Python
      •
      Other
      •9•18•2•1•Updated Aug 7, 2025Aug 7, 2025

    • shears

      Public
      shears are more powerful scissors
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•7•1•Updated Jul 25, 2025Jul 25, 2025

    • meRanTK

      Public
      methylated RNA Tool Kit
      Perl
      •
      Other
      •1•8•5•0•Updated Jul 14, 2025Jul 14, 2025

    • nextNEOpi

      Public
      nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
      pipelinenextflowneoantigens
      pipelinenextflowneoantigens
      Nextflow
      •
      Other
      •28•90•5•0•Updated Jun 6, 2025Jun 6, 2025

    • DoseRider

      Public
      DoseRider advances toxicogenomics by applying mixed models with cubic splines to analyze nonlinear dose-response relationships at the pathway level.
      R
      •
      MIT License
      •0•5•0•0•Updated Apr 14, 2025Apr 14, 2025

    • downloader

      Public
      Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)
      Nextflow
      •6•9•0•0•Updated Mar 27, 2025Mar 27, 2025

    • luca

      Public
      Single-cell Lung Cancer Atlas with 1.2M cells
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •30•92•1•0•Updated Jan 19, 2025Jan 19, 2025

    • loncova_mcb_2024

      Public
      Code to for the MCB chapter in "Immuno-oncology and immunotherapy" (Loncova et al. 2024)
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • plattner_mcb_2024

      Public
      Code for the MCB chapter in "Immuno-oncology and immunotherapy" (Plattner et al. 2024)
      Jupyter Notebook
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • GDF15_TCGA

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

    • OvRSeq

      Public
      OvRSeq is an R package for analyzing RNA sequencing data from ovarian cancer patients.
      R
      •1•1•0•0•Updated Feb 20, 2024Feb 20, 2024

    • hgsoc

      Public
      Code Repository for 'Integrated immunogenomic analyses of high-grade serous ovarian cancer reveal vulnerability to combination immunotherapy'
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 27, 2023Nov 27, 2023

    • plattner_2023

      Public
      Code to reproduce figures from Plattner, Lamberti, Blattmann, Kirchmair et al. iScience 2023
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Nov 17, 2023Nov 17, 2023

    • miopy

      Public
      HTML
      •
      Other
      •1•1•0•0•Updated Oct 19, 2023Oct 19, 2023

    • kirchmair_2023

      Public
      R
      •0•0•0•0•Updated Oct 7, 2023Oct 7, 2023

    • nmp-liver

      Public
      Single cell analysis of donor livers pre- and post machine perfusion
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•8•0•0•Updated May 23, 2023May 23, 2023

    • indelicato_2023

      Public
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 13, 2023Mar 13, 2023

    • NeoFuse

      Public
      NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.
      Shell
      •
      GNU General Public License v3.0
      •9•21•2•0•Updated Aug 9, 2022Aug 9, 2022

    • nf-deseq2

      Public
      A RNA-seq differential expression analysis pipeline downstream of nf-core/rnaseq.
      R
      •
      BSD 2-Clause "Simplified" License
      •5•7•15•2•Updated Jun 30, 2022Jun 30, 2022

    • current-topics-bioinformatics-lecture

      Public
      Shell
      •5•10•0•0•Updated Jan 20, 2022Jan 20, 2022

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.9k•0•0•0•Updated Oct 22, 2021Oct 22, 2021

    • borst2021

      Public
      single-cell analysis for the Borst et al. (2021) paper.
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Oct 16, 2021Oct 16, 2021

    • duurland2021_paper

      Public
      Single-cell analysis for Duurland et al.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Sep 28, 2021Sep 28, 2021
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