Uppsala University, Department of Medical Sciences, Molecular Precision Medicine

Molecular Precision Medicine research group and the SNP&SEQ Technology Platform

Sweden

Pinned Repositories

checkQC
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
Language:Python24 12 2316
clarity-ext
Extensions for Clarity
Language:Python6 10 18
emil
Developer-friendly predictive modeling framework
Language:R4 14 50
epiqc
Language:R2 11 02
fastq_demux
Demultiplex Illumina FASTQ files
Language:Python3 6 60
hercules
Language:Scala23
irma-scripts
Stand-alone scripts deployed to Irma
Language:Python0 9 06
Nordlund-ALL-subtyping
DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia
Language:R2 14 01
Nordlund-Backlin-2013
Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
Language:R6 14 14
sisyphus
Pipeline scripts for processing and QC of Illumina HiSeq and MiSeq data
Language:Perl2 16 3010

Uppsala University, Department of Medical Sciences, Molecular Precision Medicine's Repositories

Molmed/checkQC
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
Language:Python24 12 2316
Molmed/clarity-ext
Extensions for Clarity
Language:Python6 10 18
Molmed/fastq_demux
Demultiplex Illumina FASTQ files
Language:Python3 6 60
Molmed/epiqc
Language:R2 11 02
Molmed/Krali-Palle_2021
Language:Jupyter Notebook1 7 01
Molmed/projman_filler
Application used to populate ProjMan with runfolder data
Language:Python1 5 21
Molmed/seqreports
This is a Nextflow pipeline for generating sequencing reports for the SNP&Seq Technology platform, NGI Uppsala, SciLifelab Genomics.
Language:Python1 9 110
Molmed/CopyNumber450kCancer
CopyNumber450kCancer R package
Language:R0 6 12
Molmed/irma-scripts
Stand-alone scripts deployed to Irma
Language:Python0 9 06
Molmed/Krali_2023
Language:Jupyter Notebook0 4 00
Molmed/multiseq-ds
Language:R0 11 00
Molmed/alloy
ALLoy is a user-friendly web application that allows the rapid subtyping of ALL patients using ALLIUM (ALL subtype Identification Using Machine learning)
Language:HTML5 0
Molmed/db_dev_workflow
A set of db-procedures and sql scripts related to the Chiasma system
Language:TSQL10 01
Molmed/Equine_Asthma_Cell_Atlas
Analysis scripts for the Equine Asthma Cell Atlas project
Language:R
Molmed/gene-thesaurus
Translates from older gene name aliases to the current HGNC standard gene name
Language:Python4 0
Molmed/genologics
Python interface to the GenoLogics LIMS server via its REST API.
Language:Python9 01
Molmed/PlattformOrdMan
Internal system to control purchase of products
Language:C#10 01
Molmed/pSS_scRNAseq
Code for Sjögren's scRNA-seq analysis
Language:R1 0
Molmed/REH
Analysis scripts for the REH cell line.
Language:Python4 0
Molmed/release-ccharp
Tool for deploying C# applications (windows)
Language:Python10 01
Molmed/release-tools
Tools for a build/deployment pipeline
Language:Python8 01
Molmed/seq_ref_sync
Language:C#7 0
Molmed/sis_style_checksums_nextflow
A Nextflow pipeline to generate sisyphus-style checksums
Language:Nextflow2
Molmed/snpseq-archive-db
REST service for storing archive metadata in SQLite db
Language:Python10 02
Molmed/snpseq-archive-upload
Rest service for handling archive uploads
Language:Python10 06
Molmed/snpseq-archive-verify
REST service for verifying uploaded archives
Language:Python10 07
Molmed/snpseq-metadata-service
Language:Python1
Molmed/snpseq_metadata
Language:Python2 0
Molmed/st2-docker
StackStorm docker-compose deployment
Language:Shell2 03
Molmed/Stouts.iptables
Ansible role which manage iptables rules
Language:Shell8 0