Discover NBISweden/LocalEGA Open Source project

Genome Assembly and Annotation Service code

216

GAAS

Perl

199

workshop-scRNAseq

Single cell RNA sequencing analysis course

Workshop in omics integration and systems biology

190

workshop_omics_integration

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

EMBLmyGFF3

NBIS/ELIXIR course: Tools for Reproducible Research

workshop-reproducible-research

A set of workflows written in Nextflow for Genome Annotation.

pipelines-nextflow

Nextflow

workshop-RNAseq

Workshop • Analysis of RNA-seq data

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

GUESSmyLT

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.

GenErode

SIB/Scilifelab autumn school in single cell omics 2019.

single-cell_sib_scilifelab

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_2021

Ancient microbiome snakemake workflow

aMeta

NBIS workshop in Neural Nets and Deep Learning

workshop-neural-nets-and-deep-learning

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

IgDiscover-legacy

Development guidlines for software within NBIS.

development-guidelines

workshop-epigenomics-RTDs

workshop website on readthedocs

raukrtemplate

Presentation & lab RMarkdown templates for RaukR course

workshop-mlbiostatistics

Whole Genome Sequenceing Structural Variation Pipelines

wgs-structvar

Nextflow

workshop-genome_assembly

workshop-ngsintro

Workshop • Intro to Bioinformatics using NGS data • 5 days

A snakemake workflow for metagenomic projects

nbis-meta

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.

TransposonPSI

Pep8

Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.

Nextflow

project_template

An example of how to organize files for a research project to increase reproducibility

Dockerfile

workshop-genome_annotation

This is the NBIS repository for the Genome Annotation Workshop.

workshop-python

sauron

Website is at:

workshop-r

Workshop • R Programming Foundations for Life Scientists • 5 days

Workshop on advanced python lead by Sergio Netotea

workshop-advanced-python

Pipelines developed within NBIS through different pipeline frameworks.

pipelines

contigtax

Taxonomic classification of metagenomic contigs

workshop-spatial

User command line interface for the SDA

sda-cli

workflow-tools-evaluation

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

Population Genomics in Practice main website

workshop-pgip

TeX

workshop_omicsint_ISMBECCB

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

NBIS Summer School • Advanced R for Bioinformatics

raukr-2024

JavaScript

fungal-trans

A Snakemake workflow for fungal metatranscriptomics

Small snakemake best practice workflow

snakemake_best_practice

Nextflow pipeline for standardised variant calls on canine genomes

K9-WGS-Pipeline

R code for variant prioritization, intended for use with Sarek

pathfindr

RaukR-2019

RaukR 2019 teaching materials

workshop-snakemake-byoc

Documentation for data submissions from life science research in public repositories

data-submission-documentation

A simple CLI for automating RKE deployments on Openstack using Terraform

rke-openstack

Reproducible research repository for NBIS project G Arnqvist 1305

ReprRes_G_Arnqvist_1305

Perl

assemblyeval-smk

Snakemake workflow for evaluation of assemblies

genome annotation course within ELIXIR

workshop-genome_annotation_elixir

transient storage service

xferticket

Short lessons, training various technologies useful to our work.

Training-Tech-shorts

TeX

vcf2cytosure

Convert VCF with structural variations to CytoSure format

workshop-plotting-in-r

Single Cell Project Based Learning

sda-services-backup

single-cell-pbl

Update of Redmine Anonymous Watchers plugin to work with redmine v3+.

redmine_anonymous_watchers

Redmine plugin for displaying users schedules.

redmine_timetables

How to use Conda and how to contribute to Bioconda

workshop-conda

Encyclopedia of Cancer Microenvironment

encam

TypeScript

module-open-science-dm-practices

Open Science module for Data Management course (carpentries style)

NBIS course Bioinformatics for Principal Investigators

workshop-bioinformatics-for-PIs

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.

Smarty

homepage_rshiny.nbis.se

homepage for rshiny.nbis.se

NBIS Summer School • Advanced R for Bioinformatics

NBIS-template-support-reports

raukr-2023

JavaScript

workshop-data-visualization-r

Materials for NBIS workshop on data visulalization

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

NBIS-UtilityCode

C++

a_johansson_2020

Åsa Johansson partner project 2020

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

assembly-project-template

SMS_4882_19_Prostate_Bulk_RNA_Seq

A cloud solution for providing workshops

workshop-in-the-cloud

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

dicom-data-visualizer

Cython talk held August 2019

theherdbook

The Herd Book

TypeScript

cython-talk

Simple redmine command line client.

rmclient

Terraform deployment of LocalEGA on openstack

LocalEGA-deploy-terraform

Elixir Excelerate Demonstrator 4.3

excelerate-demonstrator-4.3

HCL

redmine_surveys_notifier

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

Introduction into kmer analysis

workshop-kmer-analysis

Helm chart for grand challenge

canvas-integrations

gc-bp-helm

R Programming Foundations for Life Scientists

web-grav-content

JavaScript

Rcourse

sms6012_CZIomicsint

Introduction to Bioinformatics Using NGS Data

NGScourse

course_chipseq

web-server implementation for topcons2

predictprotein-webserver-topcons2

ejprd

NBIS peer review track project template

CMK-NBIS-PRT-project-template

pipelines-bpipe

NBIS bpipe pipelines framework

Groovy

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.

Tool for easing the submission of data to the ENA

ENA-submission

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

confluence-server-to-cloud-utils

Common configuration of githubpages for workshops

100

workshop-common