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limma

Linear Models for Microarray Data

lncpipereporter

An R package for automatically aggregating and summarizing lncRNA analysis results.

maneline

A Nextflow pipeline to use MANE annotations with GRCh37 and optional BED files.

metabric_survival

Survival analysis using Cox PH on METABRIC data

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

multiqc_testdata

Test data for MultiQC. See https://github.com/ewels/MultiQC

mynewrepo

nanopore_gdna_cna

Copy number alteration calls for genomic DNA input to nanopore using NextFlow and Singularity

nf-pcgr

nfcore_download_singularity

nf-core tools doesn't download Singularity images properly ATOW

nrpb_methylation_annotation

nvb1fillout

Fill out NVB1 forms from CSV

nvb1shiny

Fillout NVB1 form automation

parsepcgrcpsr

Parsing of JSON files from PCGR, CPSR

perl

Repo for utility Perl scripts

r

R functions

r-iq-oq

R-IQ-OQ is an R/Sweave based program designed to serve as a foundation for the Installation Qualification (IQ) and Operational Qualification (OQ) of R (http://www.r-project.org/) when used in environments (such as regulated clinical trials) where such processes may be required.

rdl_rnaseq

BD Han2 Rat Model of Endometrial Cancer

rnafusion

RNA-seq analysis pipeline for detection gene-fusions

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rnaseq_kallisto

RNAseq with Kallisto

rnaseqkallistode

R package for DE analysis within RNAseq_kallisto_DE Nextflow pipeline

rnaseqon

R functions for use with RNAseq downstream analysis

sbatch_nxf_creator

sharc

shinysetuppostgresql

Shiny app to set up a PostgreSQL table in a database from user input of XLSX files

singularity

Singularity recipes

somatic_n-of-1

Somatic-Germline n-of-1 DNAseq Analysis

somaticvariantconsensus

In n-of-1 studies with multiple recurrences and/or metastases, somatic variants may be arbitrarily filtered unnecessarily. This method addresses this issue.