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absolute

ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38

ascat

ASCAT copy number R package

bioinformatics-tools-finder

cellxgene_vip

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

cis_immunology

conipher-wrapper

counttofpkm

Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)

dna-seq-analysis

DNA sequencing analysis notes from Ming Tang

doabsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package

docker-sge

Dockerfile to build a container with SGE installed

dockstore-cgpwgs

Dockstore implementation of CGP core WGS analysis

ezascat

Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R

genomics

Sphinx documentation source for a computational genomics tutorial.

gwas

Genome-wide Association Study (GWAS) Tutorial

hello

Web Programming with Python and JS

hg38tob37.over.chain

htseq-merge

R script for combine HTSeq outputs into one read count matrix in R

install_gistic

Install GISTIC2 by one line code; GISTIC2 docker image

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

parallelgddetect

A package to detect distinct genome doubling events which have occurred in different samples from the same tumour

phylogicndt_docker

PhylogicNDT dockcer for clonal evolution analysis

pipeline-v5

This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

pipeliner

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

preinvasive

Molecular analysis of pre-invasive lung cancer samples

pythoncourses

Learning to Program via Python, and Scientific Python for Programmers course material

rnaseq-workflow

A repository for setting up a RNAseq workflow

rnaseqshort

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

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

scp

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

scrnaseqpipeline