jemten

Bravo_ST

active

Backup of active work

BestPracticesWorkshop

Repository for the workshop "Best practices on development"

Binary-tag

bioconda-recipes

Conda recipes for the bioconda channel.

BlobFish

Differential expression analysis using DEseq2 and Salmon

BootstrapAnn

A tool for computing ASE P values based on ASEReadCounter output files

bravo-protocols

VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.

configs

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

development

Software development guidelines at Clinical Genomics. http://www.clinicalgenomics.se/development/

MIP

Mutation Identification Pipeline. Read the latest documentation:

createpanelrefs

Generate Panel of Normals, models or other similar references from lots of samples

drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

jemt

MBS

The automated protocols for Spatial transcriptomics

MegaFusion

Convert RNA fusion files to SV VCF

mitosign

mtDNA deletion and depletion signatures from wgs data

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

nf_core-tools

Python package with helper tools for the nf-core community.

python_koans

Python Koans - Learn Python through TDD

raredisease

Call and score variants from WGS/WES of rare disease patients.

RareDisease_RNA_workflow

rnaseq

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

smrnaseq

Analysis pipeline for small-RNA sequencing data.

ST_development

Non validated protocols

SVDB

structural variant database software

test-datasets

Test data to be used for automated testing with the nf-core pipelines

TIDDIT

TIDDIT - structural variant calling

trailblazer

Keep track of and manage analyses

vcf2cytosure

Convert VCF with structural variations to CytoSure format