Repositories list

• bp-sweden-web

  Public
  Website for BigPicture Sweden

  SCSS

  •

  MIT License

  •0•0•1•0•Updated Jan 8, 2025Jan 8, 2025

• theherdbook

  Public
  The Herd Book

  studbokherd-managementgenebank+ 1herd-book

  TypeScript

  •

  GNU Affero General Public License v3.0

  •1•1•30•25•Updated Jan 8, 2025Jan 8, 2025

• workshop-pgip

  Public
  Population genomics in practice main website

  TeX

  •0•1•0•0•Updated Jan 8, 2025Jan 8, 2025

• workshop-scRNAseq-devel

  Public
  Single cell RNA sequencing analysis course

  HTML

  •101•0•3•0•Updated Jan 8, 2025Jan 8, 2025

• workshop-reproducible-research

  Public
  NBIS/Elixir course: Tools for Reproducible Research

  HTML

  •

  Creative Commons Attribution 4.0 International

  •32•62•10•0•Updated Jan 8, 2025Jan 8, 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•476•18•1•Updated Jan 7, 2025Jan 7, 2025

• sda-services-backup

  Public
  neic-sda

  Go

  •1•2•1•0•Updated Jan 7, 2025Jan 7, 2025

• sda-cli

  Public
  User command line interface for the SDA

  Go

  •

  GNU Affero General Public License v3.0

  •1•5•45•0•Updated Jan 7, 2025Jan 7, 2025

• sda-uppmax-integration

  Public
  Go

  •0•0•1•0•Updated Jan 7, 2025Jan 7, 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

  •6•14•0•0•Updated Jan 6, 2025Jan 6, 2025

• urdr

  Public
  Timelogging system of NBIS

  TypeScript

  •

  GNU Affero General Public License v3.0

  •1•0•54•20•Updated Jan 6, 2025Jan 6, 2025

• fungal-trans

  Public
  A Snakemake workflow for fungal metatranscriptomics

  Python

  •

  MIT License

  •4•4•1•0•Updated Jan 6, 2025Jan 6, 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•12•1•Updated Jan 3, 2025Jan 3, 2025

• swefreq

  Public
  Swedish Frequency resource for genomics website

  javascriptangularjsmysql+ 1python

  Python

  •

  GNU General Public License v3.0

  •1•7•0•9•Updated Dec 25, 2024Dec 25, 2024

• predictprotein-webserver-common-backend

  Public
  A generic backend framwork for sequence prediction web-servers using WSDL API

  Python

  •

  MIT License

  •0•0•1•11•Updated Dec 22, 2024Dec 22, 2024

• nbis-webapp

  Public
  Hosting service for NBIS web applications during development

  Shell

  •

  MIT License

  •0•0•0•0•Updated Dec 21, 2024Dec 21, 2024

• data-submission-documentation

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

  Python

  •0•3•0•3•Updated Dec 19, 2024Dec 19, 2024

• raukr-2025

  Public
  NBIS Summer School • R Beyond the Basics

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• strobealign-evaluation

  Public
  Python

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• bp-landing-pages

  Public
  Bigpicture project dataset landing page generator

  HTML

  •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• aMeta

  Public
  Ancient microbiome snakemake workflow

  Python

  •

  MIT License

  •14•21•15•4•Updated Dec 17, 2024Dec 17, 2024

• 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 Dec 16, 2024Dec 16, 2024

• 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

  •1•3•2•2•Updated Dec 13, 2024Dec 13, 2024

• workshop-epigenomics-RTDs

  Public
  workshop website on readthedocs

  13•19•0•0•Updated Dec 9, 2024Dec 9, 2024

• copilot_proxy_demo

  Public
  A demo repo to show what Copilot sends to GitHub.

  Python

  •0•1•0•0•Updated Dec 6, 2024Dec 6, 2024

• sbpda

  Public
  This repository is public repo to share the scripts/workflows related to Spatial Biology & NBIS platforms collaborations

  Python

  •0•0•3•0•Updated Dec 5, 2024Dec 5, 2024

• Containerized-Compute-Helm-Charts

  Public
  Fork for working on CC Helm charts

  Shell

  •1•0•0•0•Updated Dec 4, 2024Dec 4, 2024

• 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•0•Updated Dec 3, 2024Dec 3, 2024

• Training-Tech-shorts

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

  TeX

  •11•4•21•6•Updated Dec 2, 2024Dec 2, 2024

• EGA-SE-user-docs

  Public
  Repository with all the information and documents for the the users of ega-se

  neic-sda

  0•1•0•0•Updated Nov 28, 2024Nov 28, 2024