Repositories list

• urdr

  Public
  Timelogging system of NBIS

  TypeScript

  •

  GNU Affero General Public License v3.0

  •1•0•55•21•Updated Mar 6, 2025Mar 6, 2025

• workshop-ngsintro

  Public
  Workshop • Intro to Bioinformatics using NGS data • 5 days

  rnaseqvariant-callingunix-shell+ 2ngs-analysisbioinformatics

  HTML

  •

  GNU General Public License v3.0

  •7•14•0•0•Updated Mar 6, 2025Mar 6, 2025

• sda-cli

  Public
  User command line interface for the SDA

  Go

  •

  GNU Affero General Public License v3.0

  •1•5•49•2•Updated Mar 6, 2025Mar 6, 2025

• workshop-scRNAseq

  Public
  Single cell RNA sequencing analysis course

  HTML

  •102•203•4•0•Updated Mar 6, 2025Mar 6, 2025

• elixir_evaluation_evaluation

  Public
  An evaluation of the ELIXIR course evaluation

  elixircourseevaluation+ 2surveynbis

  Shell

  •

  GNU General Public License v3.0

  •0•0•8•0•Updated Mar 6, 2025Mar 6, 2025

• sda-services-backup

  Public
  neic-sda

  Go

  •1•2•2•0•Updated Mar 6, 2025Mar 6, 2025

• teaching_literature_club

  Public
  NBIS' teaching literature club

  clubmeetingteaching+ 4literaturepedagogytlcnbis

  Shell

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Mar 6, 2025Mar 6, 2025

• NanoSeq

  Public
  Analysis software for Nanorate Sequencing (NanoSeq) experiments

  C++

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Mar 6, 2025Mar 6, 2025

• ML4Life

  Public
  SCSS

  •

  MIT License

  •1•0•0•0•Updated Mar 5, 2025Mar 5, 2025

• GenErode

  Public
  GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.

  Python

  •

  GNU General Public License v3.0

  •7•25•17•1•Updated Mar 5, 2025Mar 5, 2025

• sda-uppmax-integration

  Public
  Go

  •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

• sdafs

  Public
  FUSE file system driver for the sensitive data archive

  Go

  •

  MIT License

  •0•0•0•3•Updated Mar 3, 2025Mar 3, 2025

• vector-oligo-search

  Public
  Python

  •

  GNU General Public License v3.0

  •1•0•1•1•Updated Mar 3, 2025Mar 3, 2025

• workshop-reproducible-research

  Public
  NBIS/Elixir course: Tools for Reproducible Research

  HTML

  •

  Creative Commons Attribution 4.0 International

  •32•63•6•0•Updated Mar 3, 2025Mar 3, 2025

• Earth-Biogenome-Project-pilot

  Public
  An assembly workflow for analysing data in the Earth Biogenome Project pilot project.

  Nextflow

  •

  GNU General Public License v3.0

  •8•12•65•1•Updated Mar 3, 2025Mar 3, 2025

• AGAT

  Public
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

  toolkitperl-scriptsgtf+ 4gffagatstandardisationgff-format

  Perl

  •

  GNU General Public License v3.0

  •58•487•17•1•Updated Mar 1, 2025Mar 1, 2025

• bp-sweden-web

  Public
  Website for BigPicture Sweden

  SCSS

  •

  MIT License

  •0•0•1•1•Updated Feb 28, 2025Feb 28, 2025

• workshop-scRNAseq-devel

  Public
  Single cell RNA sequencing analysis course

  HTML

  •102•0•3•0•Updated Feb 28, 2025Feb 28, 2025

• sll_vr_reporting_utils

  Public
  Scripts used to dig out the data needed for the SciLifeLab and VR yearly reports.

  Python

  •1•0•0•0•Updated Feb 28, 2025Feb 28, 2025

• workshop-scrnaseq-2024

  Public
  HTML

  •0•0•0•0•Updated Feb 28, 2025Feb 28, 2025

• workshop-scrnaseq-2023

  Public
  Jupyter Notebook

  •0•0•0•1•Updated Feb 28, 2025Feb 28, 2025

• Training-Tech-shorts

  Public
  Short lessons, training various technologies useful to our work.

  HTML

  •12•4•17•0•Updated Feb 25, 2025Feb 25, 2025

• ceph_utils

  Public
  Various scripts used to setup and interact with a Ceph cluster

  Shell

  •0•1•0•0•Updated Feb 24, 2025Feb 24, 2025

• PLP_Design_Portal

  Public
  This repository contains a package to create padlock probes that target RNA directly and for developing a user-friendly.portal

  0•0•11•0•Updated Feb 20, 2025Feb 20, 2025

• assembly-project-template

  Public template
  This is a template for all assembly projects. Please read the instructions below on how to use it.

  project-templategenome-annotationgenome-analysis+ 1genome-assembly

  Shell

  •

  MIT License

  •2•3•4•1•Updated Feb 20, 2025Feb 20, 2025

• .github

  Public
  0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

• workshop-epigenomics-RTDs

  Public
  workshop website on readthedocs

  14•19•0•0•Updated Feb 19, 2025Feb 19, 2025

• fungal-trans

  Public
  A Snakemake workflow for fungal metatranscriptomics

  Python

  •

  MIT License

  •4•4•1•0•Updated Feb 18, 2025Feb 18, 2025

• PLUPP-sv-mock-server

  Public
  A mock server to improve development experience for SV apps

  JavaScript

  •0•1•0•0•Updated Feb 17, 2025Feb 17, 2025

• data-submission-documentation

  Public
  Documentation for data submissions from life science research in public repositories

  Python

  •0•3•0•5•Updated Feb 14, 2025Feb 14, 2025