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@Molmed Uppsala University, Department of Medical Sciences, Molecular Precision Medicine

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    66 repositories

    • seqreports

      Public
      This is a Nextflow pipeline for generating sequencing reports for the SNP&Seq Technology platform, NGI Uppsala, SciLifelab Genomics.
      Python
      •11•2•0•3•Updated Apr 21, 2026Apr 21, 2026

    • ngs2counts_nextflow

      Public
      A Nextflow pipeline to trigger ngs2counts on olink runfolders.
      MIT License
      •1•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • Equine_skin_scSeq

      Public
      Single-Cell RNA Sequencing of Normal Equine Skin
      R
      •0•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • release-tools

      Public archive
      Tools for a build/deployment pipeline
      Python
      •3•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • projman_filler

      Public
      Application used to populate ProjMan with runfolder data
      Python
      •
      Other
      •2•1•0•0•Updated Apr 8, 2026Apr 8, 2026

    • irma-scripts

      Public
      Stand-alone scripts deployed to Irma
      Python
      •7•1•0•0•Updated Apr 7, 2026Apr 7, 2026

    • Krali_2026_Multiomics

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 9, 2026Mar 9, 2026

    • gene-thesaurus

      Public
      Translates from older gene name aliases to the current HGNC standard gene name
      Python
      •
      MIT License
      •0•3•0•0•Updated Feb 13, 2026Feb 13, 2026

    • st2-docker

      Public
      StackStorm docker-compose deployment
      Shell
      •
      Apache License 2.0
      •167•0•0•1•Updated Feb 9, 2026Feb 9, 2026

    • checkQC

      Public
      CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
      quality-controlgenomicssequencing
      quality-controlgenomicssequencingillumina
      Python
      •
      GNU General Public License v3.0
      •17•29•10•0•Updated Nov 27, 2025Nov 27, 2025

    • Equine_cfRNA

      Public
      Cell free RNA Transcript Analysis Script for Equine Asthma at the Molecular Precision Medicine research group, Uppsala University.
      R
      •0•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • ALLCoP

      Public
      Conformal prediction for acute lymphoblastic leukemia (ALL) RNA-seq classifiers
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 2, 2025Jun 2, 2025

    • conformist

      Public
      A conformal prediction framework implementing conformal risk control, providing statistically guaranteed prediction sets for any classifier.
      Python
      •
      MIT License
      •0•3•1•0•Updated Jun 2, 2025Jun 2, 2025

    • fastq_demux

      Public
      Demultiplex Illumina FASTQ files
      Python
      •
      GNU General Public License v3.0
      •1•10•6•0•Updated May 23, 2025May 23, 2025

    • EquBAL_explorer

      Public
      Analysis scripts for the EquBAL Explorer project at the Molecular Precision Medicine research group, Uppsala University
      R
      •1•0•0•0•Updated Apr 28, 2025Apr 28, 2025

    • allium_prepro

      Public
      Tools to preprocess gene expression and DNA methylation data for prediction using the ALLIUM classifier.
      Python
      •
      MIT License
      •0•1•1•0•Updated Mar 24, 2025Mar 24, 2025

    • allium

      Public
      The ALLIUM classifier for predicting Acute Lymphoblastic Leukemia subtype using RNA-seq and DNA methylation data.
      R
      •
      MIT License
      •0•2•0•0•Updated Mar 13, 2025Mar 13, 2025

    • genologics

      Public
      Python interface to the GenoLogics LIMS server via its REST API.
      Python
      •
      MIT License
      •54•0•0•2•Updated Nov 25, 2024Nov 25, 2024

    • sis_style_checksums_nextflow

      Public
      A Nextflow pipeline to generate sisyphus-style checksums
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • Krali_2023

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • SDashboard

      Public archive
      A visualization app written in Shiny to show sequencing metrics
      R
      •
      MIT License
      •5•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • REH

      Public
      Analysis scripts for the REH cell line.
      Python
      •0•0•0•0•Updated May 23, 2024May 23, 2024

    • snpseq-metadata-service

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated May 16, 2024May 16, 2024

    • snpseq_metadata

      Public
      Python
      •1•0•0•0•Updated May 16, 2024May 16, 2024

    • clarity-ext

      Public
      Extensions for Clarity
      genomelimsdna
      genomelimsdnagenome-sequencingclarity-lims
      Python
      •8•6•0•1•Updated Feb 13, 2024Feb 13, 2024

    • pSS_scRNAseq

      Public
      Code for Sjögren's scRNA-seq analysis
      R
      •
      MIT License
      •0•1•0•0•Updated Nov 24, 2023Nov 24, 2023

    • snpseq-archive-upload

      Public
      Rest service for handling archive uploads
      Python
      •
      MIT License
      •6•0•0•0•Updated Nov 7, 2023Nov 7, 2023

    • snpseq-archive-db

      Public
      REST service for storing archive metadata in SQLite db
      Python
      •
      MIT License
      •2•0•0•0•Updated Oct 24, 2023Oct 24, 2023

    • snpseq-archive-verify

      Public
      REST service for verifying uploaded archives
      Python
      •
      MIT License
      •7•0•0•0•Updated Oct 18, 2023Oct 18, 2023

    • alloy

      Public
      ALLoy is a user-friendly web application that allows the rapid subtyping of ALL patients using ALLIUM (ALL subtype Identification Using Machine learning)
      HTML
      •
      MIT License
      •0•0•0•0•Updated Sep 21, 2023Sep 21, 2023
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