IARC bioinformatics platform

International Agency for Research on Cancer bioinformatics platform

Lyon, France

Pinned Repositories

alignment-nf
Whole Exome/Whole Genome Sequencing alignment pipeline
Language:Nextflow28 5 1213
awesome-TCGA
Curated list of TCGA resources
52 7 09
BAM-tricks
Tip and tricks for BAM files
83 9 010
IARC-nf
List of IARC bioinformatics nextflow pipelines
47 19 111
mutect-nf
Mutect pipeline with Nextflow
Language:Nextflow9 5 67
mutspec
Mutation Spectra Analysis
Language:Perl10 8 42
needlestack
Multi-sample somatic variant caller
Language:R49 11 10415
R-tricks
Tip and tricks for R
56 16 09
RNAseq-nf
RNAseq analysis pipeline
Language:HTML24 7 78
VCF-tricks
Tip and tricks for VCF files
Language:R20 14 04

IARC bioinformatics platform's Repositories

IARCbioinfo/IARC-nf
List of IARC bioinformatics nextflow pipelines
47 19 111
IARCbioinfo/alignment-nf
Whole Exome/Whole Genome Sequencing alignment pipeline
Language:Nextflow28 5 1213
IARCbioinfo/mutect-nf
Mutect pipeline with Nextflow
Language:Nextflow9 5 67
IARCbioinfo/medical_genomics_course
Material for medical genomics course
Language:Dockerfile8 5 25
IARCbioinfo/strelka2-nf
Language:Nextflow4 4 14
IARCbioinfo/purple-nf
Nextflow pipeline for CNV calling with PURPLE
Language:Nextflow3 4 11
IARCbioinfo/methylkey
Language:R2 3 03
IARCbioinfo/gama_annot-nf
Annotate VCF files with Annovar
Language:R1 2 02
IARCbioinfo/gene-fusions-nf
A nextflow pipeline to call somatic gene fusions
Language:Nextflow1 3 01
IARCbioinfo/hla-neo-nf
Pipeline to make neonantigen prediction from WGS data
Language:Perl1 5 01
IARCbioinfo/MS_panNEN_organoids
Scripts used in panNEN organoids manuscript
Language:HTML1 5 0
IARCbioinfo/RNAseq-fusion-nf
Fusion-genes discovery from RNAseq data using STAR-Fusion
Language:Nextflow1 4 01
IARCbioinfo/snpeff_annotation-nf
Annotate VCF files with SnpEff and dbSnp
Language:Nextflow1 4 02
IARCbioinfo/SpatialPCAForWSIs
Language:R1 3 0
IARCbioinfo/SComatic-nf
Nextflow pipeline to run somatic alteration calling from single-cell data using SComatic
Language:Nextflow0 4 31
IARCbioinfo/AIML-WG
Repository with scripts from IARC's Machine Learning / Artificial Intelligence working group
Language:HTML6 02
IARCbioinfo/bam2cram-nf
A repository to convert BAM->CRAM files
Language:Nextflow3 01
IARCbioinfo/bam2peaks-nf
Nextflow pipeline for peaks calling with MACS
Language:Nextflow4 0
IARCbioinfo/DPclust-nf
Nextflow workflow to run DPclust on a series of samples
Language:R5 0
IARCbioinfo/DRMetrics
Language:Jupyter Notebook3 01
IARCbioinfo/EPIC-RareCancers
IARCbioinfo/ESMOOpen_LungNENomicsCohort
2 0
IARCbioinfo/LNENBarlowTwins
Language:Jupyter Notebook2 0
IARCbioinfo/metagenomics-nf
Nextflow pipeline to perform metagenomic analyses from next-generation sequencing data
Language:Nextflow3 0
IARCbioinfo/MS_SVA
Repository with code used to produce the figures from Morrison et al. doi.org/10.1101/2023.11.23.23298821
Language:HTML3 0
IARCbioinfo/numbat-nf
Nextflow pipeline to run the numbat somatic copy number variant detection method on single-cell or spatial transcriptomics data
Language:HTML4 0
IARCbioinfo/PathonetLNEN
Language:Python2 0
IARCbioinfo/TCR-BCR-nf
A nextflow pipeline to genotype Tcell and Bcell receptors from bulk or single-cell RNAseq data
Language:Nextflow4 0
IARCbioinfo/TumorSegmentationCFlowAD
Language:HTML2 01
IARCbioinfo/WSIPreprocessing
The WSI pre-processing repository includes the patching process and the Vahadane colour normalisation method.
Language:Python2 0