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 1214
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 19 110
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/BAM-tricks
Tip and tricks for BAM files
83 9 010
IARCbioinfo/VCF-tricks
Tip and tricks for VCF files
Language:R20 14 04
IARCbioinfo/gatk4-GenotypeGVCFs-nf
Joint calling of gVCF, following GATK4 Best Practices
Language:Nextflow11 4 09
IARCbioinfo/mutspec
Mutation Spectra Analysis
Language:Perl10 8 42
IARCbioinfo/polysolver-singularity
Building a Singularity image of Polysolver
10 3 21
IARCbioinfo/mpileup2readcounts
Get per-nucleotide readcounts from samtools mpileup
Language:C++9 4 03
IARCbioinfo/gatk4-HaplotypeCaller-nf
GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping.
Language:Nextflow8 4 14
IARCbioinfo/RNAseq_analysis_scripts
Scripts for RNA seq analysis
Language:R8 5 17
IARCbioinfo/nextflow-course-2018
IARC nextflow course for pipeline users
7 4 01
IARCbioinfo/SBG-CGC_course2018
IARC course on analyzing TCGA data in the SevenBridges Genomics CancerGenomicsCloud (SBG-CGC)
Language:R6 15 74
IARCbioinfo/template-nf
Empty template for nextflow pipelines
Language:HTML5 14 32
IARCbioinfo/integration_analysis_scripts
Scripts for multi-omics integration
Language:R4 4 06
IARCbioinfo/conpair-nf
Nextflow pipeline for Conpair (concordance and contamination estimator)
Language:Nextflow3 6 0
IARCbioinfo/gatk4-DataPreProcessing-nf
Nextflow pipeline for pre-process BAM(s) with hg38 and GATK4
Language:Nextflow3 4 01
IARCbioinfo/bamsurgeon-nf
bamsurgeon with step of variant simulation encapsulated with nextflow
Language:R1 4 01
IARCbioinfo/marathon-wgs
A pipeline to study intratumor heterogeneity (ITH) with Canopy
Language:R1 4 0
IARCbioinfo/MinION_pipes
a collection of pipes developed to analyse MinION data
Language:Python1 2 0
IARCbioinfo/qualimap-nf
Language:Nextflow1 5 12
IARCbioinfo/scanMyWorkDir
Non-destructive & Informative scan of a NextFlow work folder
Language:Shell1 3 00
IARCbioinfo/acnviewer-singularity
Singularity version of acnviewer
3 0
IARCbioinfo/DraftPolisher
A tool for the polishing of draft sequences
Language:Python2 0
IARCbioinfo/ITH-nf
Language:R4 01
IARCbioinfo/Nextflow_DSL2
Repository with modules for nextflow DSL2
4 0
IARCbioinfo/platypus-nf
Platypus germline variant calling with nextflow
Language:HTML4 10
IARCbioinfo/PostAlignment-nf
Language:Nextflow4 01
IARCbioinfo/samtools_docker
Language:Dockerfile3 0
IARCbioinfo/target-seq
workflow description to call mutation with needlestack on targeted sequencing data
Language:R4 0
IARCbioinfo/TCGA_platypus-nf
nextflow pipeline to build annovar-ready tables from platypus TCGA calling
Language:Nextflow3 3
IARCbioinfo/variantflag
Merge and annotate variants from different callers
3 0
IARCbioinfo/vcf_normalization-nf
VCF normalization
Language:Shell4 3