QBiC (qbic-pipelines)'s repositories
cellranger
Nextflow pipeline wrapper for executing Cell Ranger
icgc-featurecounts
A Nextflow pipeline to run featureCounts on RNAseq BAM files on ICGC in AWS/AWS Batch
createpanelofnormals
Create panel of normals for Mutect2 & CNVKit
liver-ct-segmentation-package
mlf-core prediction package for U-Net models trained on the LiTS dataset.
pipeline-docs
Docs for QBiC pipelines
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
scvi-label-transfer
Integration of scRNA-seq datasets and cell type label transfer with scVI and scANVI
nf-core-rnaseq
This is a cloned repository, please use the original pipeline here: https://github.com/nf-core/rnaseq
intersectvcfs
Intersects Strelka2 and Mutect2 VCF files
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]`.
rts-stats-package
Statistics package for pH analysis based on root tissue segmentation
sradownloader
A pipeline to download raw data from SRA