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@qbic-pipelines QBiC (qbic-pipelines)

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    24 repositories

    • rnadeseq

      Public
      Differential gene expression analysis and pathway analysis of RNAseq data
      rnaseqpathway-analysispipelinenextflowdeseq2
      Nextflow
      •
      MIT License
      •21•32•5•1•Updated Dec 2, 2024Dec 2, 2024

    • neuromriprep

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • createpanelofnormals

      Public
      Create panel of normals for Mutect2 & CNVKit
      Nextflow
      •
      MIT License
      •1•2•0•1•Updated Nov 25, 2024Nov 25, 2024

    • vcftomaf

      Public
      Nextflow pipeline to convert VCF files into MAF files.
      Nextflow
      •
      MIT License
      •5•10•1•1•Updated Nov 25, 2024Nov 25, 2024

    • lsmquant

      Public
      Nextflow
      •
      MIT License
      •0•0•3•0•Updated Nov 13, 2024Nov 13, 2024

    • pipeline-docs

      Public
      Docs for QBiC pipelines
      12•2•0•2•Updated Nov 8, 2024Nov 8, 2024

    • variantmtb

      Public
      Nextflow
      •
      MIT License
      •1•3•6•0•Updated Oct 11, 2024Oct 11, 2024

    • querynator

      Public
      Python
      •
      MIT License
      •6•1•5•0•Updated Oct 10, 2024Oct 10, 2024

    • intersectvcfs

      Public
      Intersects Strelka2 and Mutect2 VCF files
      Nextflow
      •
      MIT License
      •1•1•0•0•Updated Apr 5, 2024Apr 5, 2024

    • root-tissue-segmentation-core

      Public
      Project to automate the segment the root tissue of A. thaliana into 5 different classes, includes automated HPO.
      Python
      •
      MIT License
      •2•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • root-tissue-analysis

      Public
      Pipeline for pH analysis of A. thaliana root tissue
      Jupyter Notebook
      •
      MIT License
      •1•1•7•0•Updated Feb 23, 2024Feb 23, 2024

    • rts-prediction-package

      Public
      Prediction package for root tissue segmentation in fluorescence microscopy images of A. thaliana
      Python
      •
      MIT License
      •0•0•0•10•Updated Mar 6, 2023Mar 6, 2023

    • cellranger

      Public
      Nextflow pipeline wrapper for executing Cell Ranger
      dockerpipelinenextflowcellranger
      Nextflow
      •
      MIT License
      •2•12•2•1•Updated Mar 8, 2022Mar 8, 2022

    • metapep

      Public
      From metagenomes to epitopes and beyond
      Nextflow
      •
      MIT License
      •1•3•14•0•Updated Jan 25, 2022Jan 25, 2022

    • rts-stats-package

      Public
      Statistics package for pH analysis based on root tissue segmentation
      0•0•0•1•Updated Dec 14, 2021Dec 14, 2021

    • liver-ct-segmentation-package

      Public
      mlf-core prediction package for U-Net models trained on the LiTS dataset.
      Python
      •
      MIT License
      •2•1•0•0•Updated Nov 2, 2021Nov 2, 2021

    • vcreport

      Public
      Nextflow
      •
      MIT License
      •3•0•2•0•Updated Oct 29, 2021Oct 29, 2021

    • scvi-label-transfer

      Public
      Integration of scRNA-seq datasets and cell type label transfer with scVI and scANVI
      Jupyter Notebook
      •0•1•0•0•Updated Jul 7, 2021Jul 7, 2021

    • nf-core-rnaseq

      Public
      This is a cloned repository, please use the original pipeline here: https://github.com/nf-core/rnaseq
      Nextflow
      •
      MIT License
      •709•0•0•0•Updated May 7, 2021May 7, 2021

    • guide-seq-container

      Public
      Dockerfile
      •1•0•0•0•Updated Feb 22, 2021Feb 22, 2021

    • sradownloader

      Public
      A pipeline to download raw data from SRA
      Nextflow
      •
      MIT License
      •4•0•1•2•Updated Jan 14, 2021Jan 14, 2021

    • nf-core-mag

      Public
      Please use the original pipeline nf-core/mag. This is just a fork to keep project results reproducible. You can add branches to this repository and tag them, which will automatically trigger a new build on dockerhub. You can run a specific tag with `nextflow run qbic-pipelines/nf-core-mag -r <tag> -profile cfc_dev --reads "*_R{1,2}.fastq.gz" [op…
      Nextflow
      •
      MIT License
      •111•0•0•0•Updated Jun 13, 2020Jun 13, 2020

    • clinvap

      Public
      Nextflow
      •
      MIT License
      •6•0•1•0•Updated Mar 31, 2020Mar 31, 2020

    • icgc-featurecounts

      Public
      A Nextflow pipeline to run featureCounts on RNAseq BAM files on ICGC in AWS/AWS Batch
      dockergenomicsnextflowreproduciblesingularityicgcbest-practice
      Nextflow
      •
      MIT License
      •4•3•0•0•Updated Aug 14, 2018Aug 14, 2018