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cellranger

Nextflow pipeline wrapper for executing Cell Ranger

clinvap

createpanelofnormals

Create panel of normals for Mutect2 & CNVKit

guide-seq-container

icgc-featurecounts

A Nextflow pipeline to run featureCounts on RNAseq BAM files on ICGC in AWS/AWS Batch

intersectvcfs

Intersects Strelka2 and Mutect2 VCF files

liver-ct-segmentation-package

mlf-core prediction package for U-Net models trained on the LiTS dataset.

lsmquant

metapep

From metagenomes to epitopes and beyond

nf-core-mag

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" [options]`.

nf-core-rnaseq

This is a cloned repository, please use the original pipeline here: https://github.com/nf-core/rnaseq

pipeline-docs

Docs for QBiC pipelines

querynator

rnadeseq

Differential gene expression analysis and pathway analysis of RNAseq data

root-tissue-analysis

Pipeline for pH analysis of A. thaliana root tissue

root-tissue-segmentation-core

Project to automate the segment the root tissue of A. thaliana into 5 different classes, includes automated HPO.

rts-prediction-package

Prediction package for root tissue segmentation in fluorescence microscopy images of A. thaliana

rts-stats-package

Statistics package for pH analysis based on root tissue segmentation

scvi-label-transfer

Integration of scRNA-seq datasets and cell type label transfer with scVI and scANVI

sradownloader

A pipeline to download raw data from SRA

variantmtb

vcftomaf

vcreport