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    • 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
      6652Updated Oct 28, 2024Oct 28, 2024
    • Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
      Python
      BSD 3-Clause "New" or "Revised" License
      27137123Updated Oct 28, 2024Oct 28, 2024
    • Single-cell analysis of Hairy Cell Leukemia samples published in Bohn et al.
      Jupyter Notebook
      0001Updated Oct 28, 2024Oct 28, 2024
    • nextNEOpi

      Public
      nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
      Nextflow
      Other
      246760Updated Oct 18, 2024Oct 18, 2024
    • crc-atlas

      Public
      Single-cell Colorectal Cancer Atlas with 4.27M cells
      Python
      1000Updated Oct 15, 2024Oct 15, 2024
    • 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
      0400Updated Oct 14, 2024Oct 14, 2024
    • R
      MIT License
      0000Updated Sep 11, 2024Sep 11, 2024
    • Code to for the MCB chapter in "Immuno-oncology and immunotherapy" (Loncova et al. 2024)
      Python
      MIT License
      0000Updated Mar 25, 2024Mar 25, 2024
    • Code for the MCB chapter in "Immuno-oncology and immunotherapy" (Plattner et al. 2024)
      Jupyter Notebook
      0000Updated Mar 22, 2024Mar 22, 2024
    • OvRSeq

      Public
      OvRSeq is an R package for analyzing RNA sequencing data from ovarian cancer patients.
      R
      1100Updated 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
      0000Updated Nov 27, 2023Nov 27, 2023
    • Code to reproduce figures from Plattner, Lamberti, Blattmann, Kirchmair et al. iScience 2023
      R
      BSD 3-Clause "New" or "Revised" License
      0000Updated Nov 17, 2023Nov 17, 2023
    • luca

      Public
      Single-cell Lung Cancer Atlas with 1.2M cells
      Python
      BSD 3-Clause "New" or "Revised" License
      175810Updated Nov 3, 2023Nov 3, 2023
    • miopy

      Public
      HTML
      Other
      1100Updated Oct 19, 2023Oct 19, 2023
    • R
      0000Updated Oct 7, 2023Oct 7, 2023
    • mio

      Public
      HTML
      1002Updated Aug 21, 2023Aug 21, 2023
    • nmp-liver

      Public
      Single cell analysis of donor livers pre- and post machine perfusion
      Python
      BSD 3-Clause "New" or "Revised" License
      2500Updated May 23, 2023May 23, 2023
    • R
      BSD 3-Clause "New" or "Revised" License
      0000Updated Mar 13, 2023Mar 13, 2023
    • meRanTK

      Public
      methylated RNA Tool Kit
      Perl
      Other
      1740Updated Sep 27, 2022Sep 27, 2022
    • 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
      91720Updated 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
      56152Updated Jun 30, 2022Jun 30, 2022
    • For now, redirect to ICBI website.
      HTML
      0000Updated May 14, 2022May 14, 2022
    • Shell
      5800Updated Jan 20, 2022Jan 20, 2022
    • Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)
      Nextflow
      5800Updated Nov 22, 2021Nov 22, 2021
    • R script to perform DE and Pathway enrichment analysis based on the output of nf-core/rnaseq
      R
      0200Updated Nov 17, 2021Nov 17, 2021
    • Conda recipes for the bioconda channel.
      Shell
      3.3k000Updated 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
      0100Updated Oct 16, 2021Oct 16, 2021
    • Single-cell analysis for Duurland et al.
      Python
      BSD 3-Clause "New" or "Revised" License
      0100Updated Sep 28, 2021Sep 28, 2021
    • single-cell analysis for the Abdulrahman et al. (2021) paper.
      Nextflow
      BSD 3-Clause "New" or "Revised" License
      0100Updated Sep 9, 2021Sep 9, 2021
    • quanTIseq

      Public
      a computational pipeline for the quantification of the Tumor Immune contexture from human RNA-seq data
      R
      101810Updated Jun 16, 2021Jun 16, 2021