phewas

Performs a PheWAS analysis & generates a Manhattan plot using the PheWAS R package

plant-rnaseq

Nextflow pipeline to analyse gene expression in plants

plink-minimal-nextflow-example

Minimal Nextflow pipeline that converts VCF files to PLINK binary fileset

prs

Polygenic Risk Scores Pipeline to calculate genetic risk score for any given phenotype/trait (using PRSice)

qc-dsl2

Minimal DSL2 Nextflow pipeline to run quality control (QC) using FastQC & MultiQC

qc-nf

Template Nextflow pipeline to run quality control (QC) on FastQ files using FastQC & generate an output HTML report using MultiQC

qtlmap

Portable eQTL analysis pipeline used by the eQTL Catalogue

r_vs_excel_workshop

relate

Genomics Englands' Ancestry and Relatedness inference workflow

releasethekraken

rgi

Antimicrobial resistance gene identification through CARD's Resistance Gene Identifier

rmats-nf

A pipeline to retrieve RNA sequencing data from SRA, perform alignment with hisat2 and characterize splicing events with rMATS 3.2.5.

rnadeseq

Differential gene expression analysis and pathway analysis of RNAseq data

rnafusion

RNA-seq analysis pipeline for detection gene-fusions

rnaseq

rnaseq-1

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

rnaseq-nf

A proof of concept of RNAseq pipeline

rnaseq_civet

rnatoy

A proof of concept RNA-Seq pipeline with Nextflow

roary

Pan-genome nextflow pipeline which uses fasta input files for Prokka and Roary before generating visualisations

saige

sanger-demo-rnaseq

sarek

An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing

sars-cov-2

Data code collection links for SARS-CoV-2

scalling-websockets-example

Scaling WebSockets example throughout multiple node servers using redis, socket.io and nginx or haproxy.

sci

script-nf

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

sentieontest

This is a repo for testing sentieon in deploit

seq-format-validation-old

Workflows for validating sequence data formats