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BAM-tricks
Tip and tricks for BAM filesR-tricks
Tip and tricks for Rawesome-TCGA
Curated list of TCGA resourcesneedlestack
Multi-sample somatic variant callerIARC-nf
List of IARC bioinformatics nextflow pipelinesalignment-nf
Whole Exome/Whole Genome Sequencing alignment pipelineRNAseq-nf
RNAseq analysis pipelineVCF-tricks
Tip and tricks for VCF filespolysolver-singularity
Building a Singularity image of Polysolvermutspec
Mutation Spectra Analysisgatk4-GenotypeGVCFs-nf
Joint calling of gVCF, following GATK4 Best Practicesmutect-nf
Mutect pipeline with NextflowRNAseq_analysis_scripts
Scripts for RNA seq analysisnextflow-course-2018
IARC nextflow course for pipeline usersmedical_genomics_course
Material for medical genomics coursegatk4-HaplotypeCaller-nf
GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping.GDC-tricks
tricks to use the Genomics Data Commons portal from the National Cancer InstituteGviz_multiAlignments
R script for multiple BAM alignments viewing using Gviz (bioconductor package)SBG-CGC_course2018
IARC course on analyzing TCGA data in the SevenBridges Genomics CancerGenomicsCloud (SBG-CGC)table_annovar-nf
annotation of variants with annovar and nextflowtemplate-nf
Empty template for nextflow pipelinesstrelka2-nf
GVCF_pipeline-nf
Nextflow pipeline for generate GVCF from BAM with GenomeAnalysisTK with step of realignmentabra-nf
Nextflow pipeline for ABRA (Assembly Based ReAligner)integration_analysis_scripts
Scripts for multi-omics integrationGATK-Alignment-nf
Perform bwa alignment and pre-processing following GATK best practicespurple-nf
Nextflow pipeline for CNV calling with PURPLEImputation-nf
Imputation pipelinegatk4-DataPreProcessing-nf
Nextflow pipeline for pre-process BAM(s) with hg38 and GATK4conpair-nf
Nextflow pipeline for Conpair (concordance and contamination estimator)MESOMICS_data
Data and scripts associated with MESOMICS paper and data noteaddreplacerg-nf
Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM filemethylkey
facets-nf
Pipeline using facets for fraction and copy number estimate from tumor/normal sequencingnextflow-hackathon-2017
ampliconarchitect-nf
Nextflow pipeline to discover ecDNA on cancer genomesITH_pipeline
Pipeline to study intra tumor heterogeneity using HATCHet, DeCiFer and ClonEvolstrelka-nf
EGA-tricks
tricks to use the European Genome-Phenome Archive from the European Bioinformatics InstituteCODEX-nf
Pipeline for copy number variant calling from Whole Exome sequencing data using CODEXNGSCheckMate-nf
Nextflow pipeline to detect matched BAMs with NGSCheckMatefastqc-nf
RF-mut-f
A random forest implementation to filter germline mutations of tumor-only samplesLiftOver-nf
Convert BED/VCF files between two genomes with nextflowEPIDRIVER2020
Scripts writen for EPIDERIVER projectbamsurgeon-nf
bamsurgeon with step of variant simulation encapsulated with nextflowqualimap-nf
intro-cancer-genomics
Introduction to cancer genomicsLSF-tricks
Tip and tricks for IBM platform LSF HPC job schedulerscanMyWorkDir
Non-destructive & Informative scan of a NextFlow work foldergene-fusions-nf
A nextflow pipeline to call somatic gene fusionswsearch-nf
Microbiome analysis with usearch, vsearch and phyloseqbam_realignment-nf
bam realignment with samtools, bwa and sambambabametrics-nf
Nextflow pipeline to compute average metrics from reads that overlap a given set of positionsssvht
A set of scripts to call somatic structural variantsmpileup-nf
Nextflow pipeline for coverage computation with samtools mpileup (bed parallelization)snpeff_annotation-nf
Annotate VCF files with SnpEff and dbSnpPVAmpliconFinder
IARC-SLC-meetings
IARC Synergie Lyon Cancer bioinformatics meetings reportsmarathon-wgs
A pipeline to study intratumor heterogeneity (ITH) with CanopySpatialPCAForWSIs
HaloAE
Unsupervised anomaly detection model using a Halonet auto-encoder.PRSice-nf
Pipeline to compute polygenic risk scoresdata_test
Small data files to test IARC nextflow pipelinesLove Open Source and this site? Check out how you can help us