CD2H gitForager

Uppsala University, Department of Medical Sciences, Molecular Medicine

Login: Molmed

Company: null

Location: Sweden

email:

Blog: www.molmed.se

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Repositories

arteria-packs: StackStorm packs to automate sequencing center operations
Backlin-2017: null
Berglund-Lindqvist-2013: null
build-scripts: Contains the build-scripts Python tool, for shared tasks between builds, e.g. building documentation from source
checkQC: CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
ChiasmaBulkFileService: Web service for Chiasma, handling large files with genotype results
ChiasmaDeposit: Auxilliary client for Chiasma, placing plates and tubes in right location at lab with use of a barcode scanner.
chiasma-docs: Documents for programs related to Chiasma
ChiasmaResultService: Web service used by the Chiasma system to upload genotyping results from instruments.
ChiasmaSQL: A set of db-procedures and sql scripts related to the Chiasma system
ChiasmaTools: A set of small programs that are refered to in the SNP&SEQ quality system
clarity-ext: Extensions for Clarity
clarity-provision: Rough Ansible playbooks for provisioning Clarity LIMS
clarity-selenium: null
CustomerReports: A reporting service that is used by Chiasma, showing customer reports with genotyping statistics.
delivery: A delivery script created for UGC, which wraps the necessary Supr interactions and mover
emil: Developer-friendly predictive modeling framework
ExportR: Project statistics export utility
FPdatabase: Client for loading results from the FP instrument. (Visual Basic)
genologics: Python interface to the GenoLogics LIMS server via its REST API.
hercules: null
MachineEncrypt: Generating encrypted passwords for windows apps (Chiasma)
Marincevic-2017: Code accompanying the manuscript "Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles, by Marincevic et. al."
molmed.github.io: Hosting web content
Nordlund-ALL-subtyping: DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia
Nordlund-Backlin-2013: Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
piper: A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper
PlattformOrdMan: Internal system to control purchase of products
ProjMan: Scripts and modules for interacting with the ProjMan database
projmanr: A R package that can be used to access the ProjMan database
release-ccharp: Tool for deploying C# applications (windows)
release-tools: Tools for a build/deployment pipeline
role_hercules: Public Ansible role for deploying Hercules
SDashboard: A visualization app written in Shiny to show sequencing metrics
sisyphus: Pipeline scripts for processing and QC of Illumina HiSeq and MiSeq data
SNPQualityAnalysisTool: Analysis of SNP results provided by Chiasma
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
Stouts.iptables: Ansible role which manage iptables rules

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.