Explore @molgenis Open Source projects

MOLGENIS - open source solutions for scientific data (@molgenis)

molgenis

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systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool

molgenis

MOLGENIS - for scientific data: management, exploration, integration and analysis.

NIPTeR

R Package for Non Invasive Prenatal Testing (NIPT) analysis

molgenis-pipelines

Pipelines for NGS, imputation, gwas, ...

capice

vip

Variant Interpretation Pipeline

molgenis-legacy

The MOLGENIS Software generator tool for creating Dynamic Software Infrastructure used in the Life Sciences

CoNVaDING

Copy Number Variation Detection In Next-generation sequencing Gene panels was designed for small (single-exon) copy number variation (CNV) detection in high coverage next-generation sequencing (NGS) data

molgenis_apps-legacy

MOLGENIS Advanced Application and Computation Framework for the Life Sciences

scRNA-seq

cluster-utils

Collection of utilities / helper scripts to make life easier on our HPC clusters.

NGS_DNA

NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC

ngs-utils

Collection of notes and scripts related to NGS

molgenis-emx2

MOLGENIS EMX2, the latest version of the MOLGENIS data platform.

molgenis-js-rsql

RSQL javascript tools for transforming, encoding and parsing of strings to RSQL and vice versa

1M-cells

This is the repository which contains the code that was used to generate the results and figures of the “Single-cell RNA-sequencing reveals widespread personalized, context-specific gene expression regulation in immune cells” paper (https://doi.org/10.1038/s41467-022-30893-5)

vite-plugin-inline

Vite plugin that embeds .js and .css as base85 data

ansible-pipelines

molgenis-tools-commander

A command line interface for MOLGENIS

molgenis-service-armadillo

Armadillo; a DataSHIELD implementation, part of the MOLGENIS suite

molgenis-frontend

Frontend code for MOLGENIS

PICALO

eQTL interaction optimization using expectation maximization

molgenis-r-auth

Discover and authenticate against an OpenID server from R

NGS_Automated

vip-report-template

Report template for Variant Call Format (VCF) Report generator

vip-inheritance-matcher

annotates VCF samples with denovo and possible compound flags and matching inheritance modes

molgenis-compute

MOLGENIS Compute is a framework for bioinformatics which enables large scale data and computational workflow management in a distributed execution environment.

vip-decision-tree

Decision tree module for the Variant Interpretation Pipeline (vip)

NGS_RNA

gavin-plus

A platform for standardized modular downstream genome analysis.

docker

Dockerfiles and docker-compose for MOLGENIS

ontocat

OntoCat - Ontology Common API Tasks

Graph2VR

Visualising / Exploring Linked Data (SPARQL Construct queries) in Virtual Reality.

molgenis-app-biobank-explorer

Vue application for the biobank explorer; A card detail view on BBMRI biobank - collection data

gavin

Gene specific calibrations for CADD scores based on ClinVar, ExAC and SnpEff

hadoop-pipeline

Implementation of a hadoop (map-reduce) Next-Generation Sequencing pipeline for fast single sample genetic diagnostics.

molgenis-r-armadillo

Client to manage shared files in the MOLGENIS Armadillo suite from R

molgenis-tools-emx-downloader

Stand alone tool to download data in EMX format from molgenis servers

asterix

Automated PGx pipeline

molgenis-selenium

Selenium tests for molgenis.

molgenis-app-genenetwork

vip-report-api

Report API for Variant Call Format (VCF) Report templates

vip-report-vcf

TypeScript VCF library with support for both reading and writing

molgenis-imputation

Rapid generation of genetic imputation scripts for grid/cluster/local environments

molgenis-app-lifecycle

App for the LifeCycle catalogue

molgenis-app-autobetes

molgenis-autobetes server

vip-report

Report generator for Variant Call Format (VCF) files

GAP

Genotyping Array Pipeline

molgenis-expressions

Library to parse and evaluate simple expressions

molgenis-ops-helm

Operations Helm charts to deploy build infrastructure on Kubernetes

metabrain

Various scripts to process RNAseq data for brain eQTL analysis

molgenis-r-client

MOLGENIS R client package

molgenis-apps-core

Core molgenis user interface

molgenis_tools-legacy

Standalone runnable tools compiled into JARs with manual, test, example and sources

vip-inheritance

Imputation

molgenis-cargo

Easily run existing MOLGENIS releases on your local machine

VaSeBuilder

Validation Set Builder

capice-resources

Repository for resource files for CAPICE and updating CAPICE model

AGCT

Array Genotyping Conversion Tool

molgenis-ui-filter

Filter components

molgenis-app-snp-visualization

Application for visualising snp (single-nucleotide polymorphism) data using javascript

vue-pdfium

Vue -> HTML -> Puppeteer PDF rendering service

sc-MetaBrain-consortium

molgenis-tools-cmd-annotators

runnable jar to run the molgenis annotators

projects-solve-rd

All things related to maintaining the RD3 database

methylationnetwork

Jupyter Notebook

vcf-io

Variant Call Format (VCF) reader and writer Java library

molgenis-app-pipeline-dashboard

A MOLGENIS 'Track & Trace' dashboard for analysis pipelines

PGx-pipeline

Farmacogenetics pipeline

molgenis-app-genetics

Repository containing modules and features for interacting with, searching through, and visualising genetic data

molgenis-ops-galaxy

Ansible Galaxy public files

vkgl-consensus

VKGL data sharing of variant classifications consensus

gdi-localportal

GDI implementation of Local portal: a Molgenis connected to REMS, with Keycloak and Postgres

ds-tidyverse

pgs_based_sample_mix-up_correction

ds-tidyverse-client