Discover NBISweden/beacon-api-tests Open Source project

Genome Assembly and Annotation Service code

208

GAAS

Perl

195

workshop-scRNAseq

Single cell RNA sequencing analysis course

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

176

EMBLmyGFF3

NBIS/ELIXIR course: Tools for Reproducible Research

workshop-reproducible-research

Workshop in omics integration and systems biology

workshop_omics_integration

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

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

SIB/Scilifelab autumn school in single cell omics 2019.

single-cell_sib_scilifelab

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

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

Presentation & lab RMarkdown templates for RaukR course

raukrtemplate

Development guidlines for software within NBIS.

development-guidelines

workshop-mlbiostatistics

Whole Genome Sequenceing Structural Variation Pipelines

wgs-structvar

Nextflow

workshop-epigenomics-RTDs

workshop website on readthedocs

workshop-genome_assembly

nbis-meta

A snakemake workflow for metagenomic projects

Workshop • Intro to Bioinformatics using NGS data • 5 days

workshop-ngsintro

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

Earth-Biogenome-Project-pilot

Nextflow

project_template

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

Dockerfile

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.

Pep8

workshop-python

workshop-genome_annotation

This is the NBIS repository for the Genome Annotation Workshop.

sauron

Website is at:

workshop-r

Workshop • R Programming Foundations for Life Scientists • 5 days

Pipelines developed within NBIS through different pipeline frameworks.

pipelines

contigtax

Taxonomic classification of metagenomic contigs

Workshop on advanced python lead by Sergio Netotea

workshop-advanced-python

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

workflow-tools-evaluation

A Snakemake workflow for fungal metatranscriptomics

fungal-trans

Nextflow pipeline for standardised variant calls on canine genomes

K9-WGS-Pipeline

User command line interface for the SDA

sda-cli

LocalEGA

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

Small snakemake best practice workflow

snakemake_best_practice

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"

R code for variant prioritization, intended for use with Sarek

pathfindr

RaukR-2019

RaukR 2019 teaching materials

Training-Tech-shorts

Short lessons, training various technologies useful to our work.

TeX

data-submission-documentation

Documentation for data submissions from life science research in public repositories

workshop-spatial

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

workshop-plotting-in-r

workshop-snakemake-byoc

Single Cell Project Based Learning

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

synteny_plots_with_jcvi

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

module-open-science-dm-practices

Open Science module for Data Management course (carpentries style)

NBIS course Bioinformatics for Principal Investigators

workshop-bioinformatics-for-PIs

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

NBIS-template-support-reports

NBIS-UtilityCode

C++

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

Convert VCF with structural variations to CytoSure format

vcf2cytosure

Introduction into kmer analysis

workshop-kmer-analysis

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

sda-services-backup

theherdbook

The Herd Book

TypeScript

cython-talk

Simple redmine command line client.

rmclient

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

redmine_surveys_notifier

Terraform deployment of LocalEGA on openstack

LocalEGA-deploy-terraform

Elixir Excelerate Demonstrator 4.3

excelerate-demonstrator-4.3

HCL

canvas-integrations

snakemake-workflow-tool

How to package up a Snakemake workflow as a command-line tool

Helm chart for grand challenge

gc-bp-helm

Introduction to Bioinformatics Using NGS Data

web-grav-content

JavaScript

NGScourse

R Programming Foundations for Life Scientists

Rcourse

sms6012_CZIomicsint

course_chipseq

web-server implementation for topcons2

predictprotein-webserver-topcons2

NBIS bpipe pipelines framework

pipelines-bpipe

Groovy

aida-data-hub

AIDA Data Hub Scrum team board

a_johansson_2020

Åsa Johansson partner project 2020

Repository for Data Management training session modules

data-management-gym

ENA-submission

Tool for easing the submission of data to the ENA

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

workshop-common

A django based web-server platform suitable for schedualling time consuming jobs only at the remote computational node

predictprotein-webserver-pconsc3

Snakemake workflow for non-model organism analyses

manticore-smk

NBIS Summer School • Advanced R for Bioinformatics

raukr-2023

JavaScript

100

workshop-data-visualization-r

Materials for NBIS workshop on data visulalization