Short Tandem Repeat disease loci resource

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

GWAS Tutorial for Beginners

A comprehensive cancer DNA/RNA analysis and reporting pipeline

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

RNA-seq analysis pipeline for detection of gene-fusions

Java utilities for Bioinformatics

Query language for filtering SAM/BAM reads

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

Bioinformatics containers

FusionInspector code

tools for working with genome variation graphs

Applied Computational Genomics Course at UU: Spring 2020

A collection of command line tools for working with sequencing data

SigProfilerExtractor

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED fil…

STAR-Fusion codebase

Non-Invasive Prenatal Testing (NIPT) size selection and deduplication pipeline

Official repository for the Deep Docking protocol

Sample web application for the AWS DevOps Engineer Learning Path.

Identification of gene-fusions, including EML4-ALK

Useful bash one-liners for bioinformatics.

Python program designed to reconstruct immunoglobulin gene rearrangements and oncogenic translocations from WGS, WES and capture NGS in lymphoid neoplasms.