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adv-oop-in-r

Source code for 'Advanced Object-Oriented Programming in R' by Thomas Mailund

aliceflow

NextFlow framework to streamline the Genalice variant call pipeline

bendola

Creating and visualising allele phase graphs form HLA genotypes

bioconda-recipes

Conda recipes for the bioconda channel.

btb-scripts

Collection of ad-hoc scripts for BTB

caw-containers

Containers for CAW

configs

Config files used to define parameters specific to compute environments at different Institutions.

genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)

gens

A web-based interactive tool to visualize genomic copy number profiles from WGS data

hapl-o-mat

A software for haplotype inference

hello-ngi-engine

A sample engine for SciLifeLab NGI pipeline

icing

An attempt to make HLA typing from OxfordNanopore reads (MinION platform)

kshdeath

ngb

New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support

ngi-smrnaseq

Nextflow Small RNA Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

ngi_pipeline

Code driving the production pipeline at SciLifeLab

pairfastq

Pairing Illumina FASTQ files

pathfindr

R code for variant prioritization, intended for use with Sarek

ponpom

Effect of PON (Panel Of Normals) on somatic variant calls

primeula

Toy project to visualise prime numbers in a fancy way

rnafusion

RNA-seq analysis pipeline for detection gene-fusions

rxdock

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout c0c3a3a after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

sarek

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

sarek.pathfindr

Scoring and ranking somatic and germline variations for cancer research

scout

VCF visualization interface

simpanel

Simulating a tumour gene panel for NGS

smallref

Small human reference for tests

stellarium-skycultures

Sky Cultures for Stellarium

szilvajuhos.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

vcffuse