IARC bioinformatics platform

IARC-nf

List of IARC bioinformatics nextflow pipelines

alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

mutect-nf

Mutect pipeline with Nextflow

medical_genomics_course

Material for medical genomics course

strelka2-nf

MESOMICS_data

Data and scripts associated with MESOMICS paper and data note

purple-nf

Nextflow pipeline for CNV calling with PURPLE

methylkey

gama_annot-nf

Annotate VCF files with Annovar

gene-fusions-nf

A nextflow pipeline to call somatic gene fusions

hla-neo-nf

Pipeline to make neonantigen prediction from WGS data

MS_panNEN_organoids

Scripts used in panNEN organoids manuscript

RNAseq-fusion-nf

Fusion-genes discovery from RNAseq data using STAR-Fusion

snpeff_annotation-nf

Annotate VCF files with SnpEff and dbSnp

SpatialPCAForWSIs

SComatic-nf

Nextflow pipeline to run somatic alteration calling from single-cell data using SComatic

AIML-WG

Repository with scripts from IARC's Machine Learning / Artificial Intelligence working group

bam2cram-nf

A repository to convert BAM->CRAM files

bam2peaks-nf

Nextflow pipeline for peaks calling with MACS

DPclust-nf

Nextflow workflow to run DPclust on a series of samples

DRMetrics

ESMOOpen_LungNENomicsCohort

LNENBarlowTwins

metagenomics-nf

Nextflow pipeline to perform metagenomic analyses from next-generation sequencing data

MS_SVA

Repository with code used to produce the figures from Morrison et al. doi.org/10.1101/2023.11.23.23298821

numbat-nf

Nextflow pipeline to run the numbat somatic copy number variant detection method on single-cell or spatial transcriptomics data

PathonetLNEN

TCR-BCR-nf

A nextflow pipeline to genotype Tcell and Bcell receptors from bulk or single-cell RNAseq data

TumorSegmentationCFlowAD

WSIPreprocessing

The WSI pre-processing repository includes the patching process and the Vahadane colour normalisation method.