AGAT
Another Gtf/Gff Analysis ToolkitMrBayes
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:excelerate-scRNAseq
Single RNA-seq data analysis with R (Finland, May, 2019)GAAS
Genome Assembly and Annotation Service codeworkshop-scRNAseq
Single cell RNA sequencing analysis courseEMBLmyGFF3
An efficient way to convert gff3 annotation files into EMBL format ready to submit.workshop-reproducible-research
NBIS/ELIXIR course: Tools for Reproducible Researchworkshop_omics_integration
Workshop in omics integration and systems biologypipelines-nextflow
A set of workflows written in Nextflow for Genome Annotation.workshop-RNAseq
Workshop β’ Analysis of RNA-seq dataGUESSmyLT
An efficient way to guess the library type of your RNA-Seq data.single-cell_sib_scilifelab_2021
SciLifeLab SIB Summer School for Advanced topics in Single Cell Omics. Site: https://nbisweden.github.io/single-cell_sib_scilifelab_2021/single-cell_sib_scilifelab
SIB/Scilifelab autumn school in single cell omics 2019.GenErode
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.aMeta
Ancient microbiome snakemake workflowworkshop-neural-nets-and-deep-learning
NBIS workshop in Neural Nets and Deep LearningIgDiscover-legacy
Analyze antibody repertoires and discover new V genes from high-throughput sequencing readsraukrtemplate
Presentation & lab RMarkdown templates for RaukR coursedevelopment-guidelines
Development guidlines for software within NBIS.workshop-mlbiostatistics
wgs-structvar
Whole Genome Sequenceing Structural Variation Pipelinesworkshop-epigenomics-RTDs
workshop website on readthedocsworkshop-genome_assembly
nbis-meta
A snakemake workflow for metagenomic projectsworkshop-ngsintro
Workshop β’ Intro to Bioinformatics using NGS data β’ 5 daysEarth-Biogenome-Project-pilot
Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.project_template
An example of how to organize files for a research project to increase reproducibilityTransposonPSI
TransposonPSI involves a PSI-blast search of a protein or nucleotide sequence against a set of profiles of proteins corresponding to major clades/families of transposon Open Reading Frames.workshop-python
workshop-genome_annotation
This is the NBIS repository for the Genome Annotation Workshop.sauron
Website is at:workshop-r
Workshop β’ R Programming Foundations for Life Scientists β’ 5 dayspipelines
Pipelines developed within NBIS through different pipeline frameworks.contigtax
Taxonomic classification of metagenomic contigsworkshop-advanced-python
Workshop on advanced python lead by Sergio Netoteaworkflow-tools-evaluation
Evaluating workflow tools and formats, such as the Common Workflow Language (CWL) for possible use within NBISfungal-trans
A Snakemake workflow for fungal metatranscriptomicsK9-WGS-Pipeline
Nextflow pipeline for standardised variant calls on canine genomessda-cli
User command line interface for the SDALocalEGA
Please go to to https://github.com/EGA-archive/LocalEGA insteadsnakemake_best_practice
Small snakemake best practice workflowworkshop-pgip
Population Genomics in Practice main websiteworkshop_omicsint_ISMBECCB
Repository for the ISMB/ECCB workshop "A practical introduction to multi-omics integration and network analysis"pathfindr
R code for variant prioritization, intended for use with SarekRaukR-2019
RaukR 2019 teaching materialsdata-submission-documentation
Documentation for data submissions from life science research in public repositoriesworkshop-spatial
rke-openstack
A simple CLI for automating RKE deployments on Openstack using TerraformReprRes_G_Arnqvist_1305
Reproducible research repository for NBIS project G Arnqvist 1305assemblyeval-smk
Snakemake workflow for evaluation of assembliesworkshop-genome_annotation_elixir
genome annotation course within ELIXIRxferticket
transient storage serviceworkshop-plotting-in-r
workshop-snakemake-byoc
single-cell-pbl
Single Cell Project Based Learningredmine_anonymous_watchers
Update of Redmine Anonymous Watchers plugin to work with redmine v3+.redmine_timetables
Redmine plugin for displaying users schedules.workshop-conda
How to use Conda and how to contribute to Biocondaencam
Encyclopedia of Cancer Microenvironmentsynteny_plots_with_jcvi
Step-by-step tutorial to create synteny plots for pairs and trios of genomes using JCVI's MCScanmodule-open-science-dm-practices
Open Science module for Data Management course (carpentries style)workshop-bioinformatics-for-PIs
NBIS course Bioinformatics for Principal Investigatorscytomine-bp-helm
Helm charts for deploying cytomine (https://doc.cytomine.org/) to a kubernetes environment.homepage_rshiny.nbis.se
homepage for rshiny.nbis.seNBIS-template-support-reports
NBIS-UtilityCode
NBIS-UtilityCode: a place for bioinformatics tools and libraries, written and maintained by NBIS, the National Bioinformatics Infrastructure Sweden.assembly-project-template
This is a template for all assembly projects. Please read the instructions below on how to use it.SMS_4882_19_Prostate_Bulk_RNA_Seq
vcf2cytosure
Convert VCF with structural variations to CytoSure formatworkshop-kmer-analysis
Introduction into kmer analysisworkshop-in-the-cloud
A cloud solution for providing workshopsdicom-data-visualizer
A set of Jupyter Notebooks highlighting how to parse DICOM data using pydicom.sda-services-backup
theherdbook
The Herd Bookcython-talk
Cython talk held August 2019rmclient
Simple redmine command line client.redmine_surveys_notifier
This plugin allows to send a survey when a support issue is closedLocalEGA-deploy-terraform
Terraform deployment of LocalEGA on openstackexcelerate-demonstrator-4.3
Elixir Excelerate Demonstrator 4.3canvas-integrations
snakemake-workflow-tool
How to package up a Snakemake workflow as a command-line toolgc-bp-helm
Helm chart for grand challengeweb-grav-content
NGScourse
Introduction to Bioinformatics Using NGS DataRcourse
R Programming Foundations for Life Scientistsbeacon-api-tests
Compliance tester and test cases for Beacons.sms6012_CZIomicsint
course_chipseq
predictprotein-webserver-topcons2
web-server implementation for topcons2pipelines-bpipe
NBIS bpipe pipelines frameworkaida-data-hub
AIDA Data Hub Scrum team boarda_johansson_2020
Γ sa Johansson partner project 2020data-management-gym
Repository for Data Management training session modulesENA-submission
Tool for easing the submission of data to the ENAconfluence-server-to-cloud-utils
Various scripts used when migrating a Confluence Server instance to a Confluence Cloud instance.workshop-common
Common configuration of githubpages for workshopspredictprotein-webserver-pconsc3
A django based web-server platform suitable for schedualling time consuming jobs only at the remote computational nodemanticore-smk
Snakemake workflow for non-model organism analysesraukr-2023
NBIS Summer School β’ Advanced R for Bioinformaticsworkshop-data-visualization-r
Materials for NBIS workshop on data visulalizationLove Open Source and this site? Check out how you can help us