Discover molgenis/NIPTeR Open Source project

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

166

molgenis

Pipelines for NGS, imputation, gwas, ...

109

molgenis-pipelines

capice

Variant Interpretation Pipeline

vip

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

molgenis-legacy

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

CoNVaDING

HTML

molgenis_apps-legacy

MOLGENIS Advanced Application and Computation Framework for the Life Sciences

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

scRNA-seq

HTML

cluster-utils

Perl

NGS_DNA

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

Collection of notes and scripts related to NGS

ngs-utils

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

molgenis-emx2

Vue

molgenis-js-rsql

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

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)

1M-cells

vite-plugin-inline

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

ansible-pipelines

A command line interface for MOLGENIS

molgenis-tools-commander

CSS

molgenis-service-armadillo

Armadillo; a DataSHIELD implementation, part of the MOLGENIS suite

Frontend code for MOLGENIS

molgenis-frontend

eQTL interaction optimization using expectation maximization

PICALO

Discover and authenticate against an OpenID server from R

molgenis-r-auth

NGS_Automated

Report template for Variant Call Format (VCF) Report generator

vip-report-template

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

vip-inheritance-matcher

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

molgenis-compute

Decision tree module for the Variant Interpretation Pipeline (vip)

vip-decision-tree

NGS_RNA

A platform for standardized modular downstream genome analysis.

gavin-plus

Dockerfiles and docker-compose for MOLGENIS

docker

Dockerfile

ontocat

OntoCat - Ontology Common API Tasks

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

Graph2VR

molgenis-app-biobank-explorer

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

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

gavin

hadoop-pipeline

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

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

molgenis-r-armadillo

molgenis-tools-emx-downloader

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

asterix

Automated PGx pipeline

Selenium tests for molgenis.

molgenis-selenium

molgenis-app-genenetwork

Report API for Variant Call Format (VCF) Report templates

vip-report-api

TypeScript VCF library with support for both reading and writing

vip-report-vcf

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

molgenis-imputation

App for the LifeCycle catalogue

molgenis-app-lifecycle

molgenis-autobetes server

molgenis-app-autobetes

FreeMarker

vip-report

Report generator for Variant Call Format (VCF) files

HTML

GAP

Genotyping Array Pipeline

Library to parse and evaluate simple expressions

molgenis-expressions

Scala

molgenis-ops-helm

Operations Helm charts to deploy build infrastructure on Kubernetes

Mustache

molgenis-r-client

MOLGENIS R client package

molgenis-apps-core

Core molgenis user interface

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

molgenis_tools-legacy

vip-inheritance

Imputation

Easily run existing MOLGENIS releases on your local machine

molgenis-cargo

VaSeBuilder

Validation Set Builder

Repository for resource files for CAPICE and updating CAPICE model

capice-resources

Array Genotyping Conversion Tool

AGCT

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

molgenis-ui-filter

Filter components

Vue

molgenis-app-snp-visualization

Vue -> HTML -> Puppeteer PDF rendering service

vue-pdfium

sc-MetaBrain-consortium

runnable jar to run the molgenis annotators

molgenis-tools-cmd-annotators

projects-solve-rd

Variant Call Format (VCF) reader and writer Java library

methylationnetwork

Jupyter Notebook

vcf-io

A MOLGENIS 'Track & Trace' dashboard for analysis pipelines

molgenis-app-pipeline-dashboard

PGx-pipeline

Farmacogenetics pipeline

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

molgenis-app-genetics

Ansible Galaxy public files

molgenis-ops-galaxy

VKGL data sharing of variant classifications consensus

vkgl-consensus

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

gdi-localportal