Explore @NBISweden Open Source projects

NBIS - National Bioinformatics Infrastructure Sweden (@NBISweden)

NBISweden

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AGAT

Another Gtf/Gff Analysis Toolkit

MrBayes

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 code

workshop-scRNAseq

Single cell RNA sequencing analysis course

workshop_omics_integration

Workshop in omics integration and systems biology

EMBLmyGFF3

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

workshop-reproducible-research

NBIS/ELIXIR course: Tools for Reproducible Research

pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.

workshop-RNAseq

Workshop • Analysis of RNA-seq data

GUESSmyLT

An efficient way to guess the library type of your RNA-Seq data.

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.

single-cell_sib_scilifelab

SIB/Scilifelab autumn school in single cell omics 2019.

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/

Jupyter Notebook

aMeta

Ancient microbiome snakemake workflow

workshop-neural-nets-and-deep-learning

NBIS workshop in Neural Nets and Deep Learning

IgDiscover-legacy

Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads

development-guidelines

Development guidlines for software within NBIS.

workshop-epigenomics-RTDs

workshop website on readthedocs

raukrtemplate

Presentation & lab RMarkdown templates for RaukR course

workshop-mlbiostatistics

wgs-structvar

Whole Genome Sequenceing Structural Variation Pipelines

workshop-genome_assembly

workshop-ngsintro

Workshop • Intro to Bioinformatics using NGS data • 5 days

nbis-meta

A snakemake workflow for metagenomic projects

TransposonPSI

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.

Earth-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 reproducibility

workshop-genome_annotation

This is the NBIS repository for the Genome Annotation Workshop.

workshop-python

sauron

workshop-r

Workshop • R Programming Foundations for Life Scientists • 5 days

workshop-advanced-python

Workshop on advanced python lead by Sergio Netotea

Jupyter Notebook

pipelines

Pipelines developed within NBIS through different pipeline frameworks.

contigtax

Taxonomic classification of metagenomic contigs

workshop-spatial

Jupyter Notebook

sda-cli

User command line interface for the SDA

workflow-tools-evaluation

Evaluating workflow tools and formats, such as the Common Workflow Language (CWL) for possible use within NBIS

workshop-pgip

Population Genomics in Practice main website

workshop_omicsint_ISMBECCB

Repository for the ISMB/ECCB workshop "A practical introduction to multi-omics integration and network analysis"

raukr-2024

NBIS Summer School • Advanced R for Bioinformatics

fungal-trans

A Snakemake workflow for fungal metatranscriptomics

snakemake_best_practice

Small snakemake best practice workflow

LocalEGA

Please go to to https://github.com/EGA-archive/LocalEGA instead

K9-WGS-Pipeline

Nextflow pipeline for standardised variant calls on canine genomes

pathfindr

R code for variant prioritization, intended for use with Sarek

RaukR-2019

RaukR 2019 teaching materials

workshop-snakemake-byoc

data-submission-documentation

Documentation for data submissions from life science research in public repositories

rke-openstack

A simple CLI for automating RKE deployments on Openstack using Terraform

ReprRes_G_Arnqvist_1305

Reproducible research repository for NBIS project G Arnqvist 1305

assemblyeval-smk

Snakemake workflow for evaluation of assemblies

workshop-genome_annotation_elixir

genome annotation course within ELIXIR

xferticket

transient storage service

Training-Tech-shorts

Short lessons, training various technologies useful to our work.

vcf2cytosure

Convert VCF with structural variations to CytoSure format

workshop-plotting-in-r

sda-services-backup

single-cell-pbl

Single Cell Project Based Learning

redmine_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 Bioconda

encam

Encyclopedia of Cancer Microenvironment

module-open-science-dm-practices

Open Science module for Data Management course (carpentries style)

workshop-bioinformatics-for-PIs

NBIS course Bioinformatics for Principal Investigators

synteny_plots_with_jcvi

Step-by-step tutorial to create synteny plots for pairs and trios of genomes using JCVI's MCScan

cytomine-bp-helm

Helm charts for deploying cytomine (https://doc.cytomine.org/) to a kubernetes environment.

homepage_rshiny.nbis.se

homepage for rshiny.nbis.se

NBIS-template-support-reports

raukr-2023

NBIS Summer School • Advanced R for Bioinformatics

workshop-data-visualization-r

Materials for NBIS workshop on data visulalization

NBIS-UtilityCode

NBIS-UtilityCode: a place for bioinformatics tools and libraries, written and maintained by NBIS, the National Bioinformatics Infrastructure Sweden.

a_johansson_2020

Åsa Johansson partner project 2020

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

workshop-in-the-cloud

A cloud solution for providing workshops

dicom-data-visualizer

A set of Jupyter Notebooks highlighting how to parse DICOM data using pydicom.

Jupyter Notebook

theherdbook

cython-talk

Cython talk held August 2019

Jupyter Notebook

rmclient

Simple redmine command line client.

LocalEGA-deploy-terraform

Terraform deployment of LocalEGA on openstack

excelerate-demonstrator-4.3

Elixir Excelerate Demonstrator 4.3

redmine_surveys_notifier

This plugin allows to send a survey when a support issue is closed

workshop-kmer-analysis

Introduction into kmer analysis

canvas-integrations

gc-bp-helm

Helm chart for grand challenge

web-grav-content

Rcourse

R Programming Foundations for Life Scientists

sms6012_CZIomicsint

NGScourse

Introduction to Bioinformatics Using NGS Data

course_chipseq

predictprotein-webserver-topcons2

web-server implementation for topcons2

ejprd

CMK-NBIS-PRT-project-template

NBIS peer review track project template

pipelines-bpipe

NBIS bpipe pipelines framework

aida-data-hub

AIDA Data Hub Scrum team board

data-management-gym

Repository for Data Management training session modules

beacon-api-tests

Compliance tester and test cases for Beacons.

ENA-submission

Tool for easing the submission of data to the ENA

confluence-server-to-cloud-utils

Various scripts used when migrating a Confluence Server instance to a Confluence Cloud instance.