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

molgenis

Stars
710
Global Org. Rank 19,241 (Top 7 %)
Registered over 12 years ago
Most used languages

Java
25.3 %

Shell
15.2 %

R
13.9 %

Python
12.7 %

TypeScript
8.9 %

JavaScript
7.6 %

HTML
3.8 %

Vue 2.5 %

FreeMarker 1.3 %

Perl
1.3 %

Scala
1.3 %

C#
1.3 %

CSS
1.3 %

Mustache 1.3 %

Jupyter Notebook
1.3 %

Dockerfile
1.3 %
Location 🇳🇱 Netherlands
Country Total Rank 872
Country Ranking

FreeMarker 5

Mustache 11

R
43

Perl
57

Java
67

Vue 110

Shell
128

HTML
195

Dockerfile
264

Scala
268

CSS
279

TypeScript
535

Python
1,089

C#
1,120

JavaScript
1,873

Jupyter Notebook
1,946

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, ...

vip

Variant Interpretation Pipeline

capice

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-legacy

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

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

molgenis-emx2

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

ngs-utils

Collection of notes and scripts related to NGS

vite-plugin-inline

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

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)

molgenis-js-rsql

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

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

molgenis-r-auth

Discover and authenticate against an OpenID server from R

Graph2VR

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

PICALO

eQTL interaction optimization using expectation maximization

vip-inheritance-matcher

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

NGS_Automated

molgenis-compute

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

vip-report-template

Report template for Variant Call Format (VCF) Report generator

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

vip-report

Report generator for Variant Call Format (VCF) files

gavin

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

GAP

Genotyping Array Pipeline

molgenis-app-biobank-explorer

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

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

molgenis-expressions

Library to parse and evaluate simple expressions

molgenis-ops-helm

Operations Helm charts to deploy build infrastructure on Kubernetes

ds-tidyverse

pgs_based_sample_mix-up_correction

benchmark-gwas-prio

molgenis-r-client

MOLGENIS R client package

molgenis-apps-core

Core molgenis user interface

vip-inheritance

molgenis-cargo

Easily run existing MOLGENIS releases on your local machine

VaSeBuilder

Validation Set Builder

Imputation

capice-resources

Repository for resource files for CAPICE and updating CAPICE model

molgenis_tools-legacy

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

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-py-client

A Python client for the MOLGENIS REST API

PGx-pipeline

Farmacogenetics pipeline

molgenis-app-pipeline-dashboard

A MOLGENIS 'Track & Trace' dashboard for analysis pipelines

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-client

tsv-vcf-converter

STEMI-scRNA-seq

single cell experiments in STEMI participants