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mutsig

Mutational signature analysis of WGS data

mutspec

Mutation Spectra Analysis

needlestack

Multi-sample somatic variant caller

nextflow-course-2018

IARC nextflow course for pipeline users

nextflow-hackathon-2017

nextflow_dsl2

Repository with modules for nextflow DSL2

nf_coverage_demo

Nextflow demo plotting mean coverage over a series of BAM files

ngscheckmate-nf

Nextflow pipeline to detect matched BAMs with NGSCheckMate

octopus-nf

octopus variant caller with nextflow

platypus-nf

Platypus germline variant calling with nextflow

polysolver-singularity

Building a Singularity image of Polysolver

postalignment-nf

prsice-nf

Pipeline to compute polygenic risk scores

purple-nf

Nextflow pipeline for CNV calling with PURPLE

pvampliconfinder

qc3

QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.

qualimap-nf

quantiseq-nf

Pipeline to run software quanTIseq in parallel to quantify immune cell content from RNA-seq data

r-tricks

Tip and tricks for R

rf-mut-f

A random forest implementation to filter germline mutations of tumor-only samples

rnaseq-fusion-nf

Fusion-genes discovery from RNAseq data using STAR-Fusion

rnaseq-nf

RNAseq analysis pipeline

rnaseq-transcript-nf

Transcript-level RNA-seq analysis

rnaseq_analysis_scripts

Scripts for RNA seq analysis

samtools_docker

sbg-cgc_course2018

IARC course on analyzing TCGA data in the SevenBridges Genomics CancerGenomicsCloud (SBG-CGC)

scanmyworkdir

Non-destructive & Informative scan of a NextFlow work folder

ssvht

A set of scripts to call somatic structural variants

strelka-nf

strelka2-nf