Uppsala University, Department of Medical Sciences, Molecular Precision Medicine

checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria

clarity-ext

Extensions for Clarity

epiqc

fastq_demux

Demultiplex Illumina FASTQ files

sisyphus

Pipeline scripts for processing and QC of Illumina HiSeq and MiSeq data

Krali-Palle_2021

projman_filler

Application used to populate ProjMan with runfolder data

seqreports

This is a Nextflow pipeline for generating sequencing reports for the SNP&Seq Technology platform, NGI Uppsala, SciLifelab Genomics.

CopyNumber450kCancer

CopyNumber450kCancer R package

irma-scripts

Stand-alone scripts deployed to Irma

Krali_2023

multiseq-ds

alloy

ALLoy is a user-friendly web application that allows the rapid subtyping of ALL patients using ALLIUM (ALL subtype Identification Using Machine learning)

check-sample-submission

db_dev_workflow

A set of db-procedures and sql scripts related to the Chiasma system

gene-thesaurus

Translates from older gene name aliases to the current HGNC standard gene name

genologics

Python interface to the GenoLogics LIMS server via its REST API.

PlattformOrdMan

Internal system to control purchase of products

pSS_scRNAseq

Code for Sjögren's scRNA-seq analysis

REH

Analysis scripts for the REH cell line.

release-ccharp

Tool for deploying C# applications (windows)

release-tools

Tools for a build/deployment pipeline

seq_ref_sync

snpseq-archive-db

REST service for storing archive metadata in SQLite db

snpseq-archive-upload

Rest service for handling archive uploads

snpseq-archive-verify

REST service for verifying uploaded archives

snpseq-metadata-service

snpseq_metadata

st2-docker

StackStorm docker-compose deployment

Stouts.iptables

Ansible role which manage iptables rules