Discover molgenis/AGCT Open Source project

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

171

molgenis

R Package for Non Invasive Prenatal Testing (NIPT) analysis

111

NIPTeR

molgenis-pipelines

Pipelines for NGS, imputation, gwas, ...

Variant Interpretation Pipeline

vip

capice

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-legacy

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

MOLGENIS Advanced Application and Computation Framework for the Life Sciences

molgenis_apps-legacy

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

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

molgenis-emx2

Vue

ngs-utils

Collection of notes and scripts related to NGS

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

vite-plugin-inline

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

molgenis-js-rsql

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

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

Discover and authenticate against an OpenID server from R

molgenis-r-auth

Graph2VR

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

PICALO

eQTL interaction optimization using expectation maximization

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

vip-inheritance-matcher

NGS_Automated

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

molgenis-compute

Report template for Variant Call Format (VCF) Report generator

vip-report-template

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

Report generator for Variant Call Format (VCF) files

vip-report

HTML

gavin

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

GAP

Genotyping Array Pipeline

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

molgenis-app-biobank-explorer

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

hadoop-pipeline

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

Selenium tests for molgenis.

asterix

Automated PGx pipeline

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

molgenis-expressions

Library to parse and evaluate simple expressions

Scala

molgenis-ops-helm

Operations Helm charts to deploy build infrastructure on Kubernetes

Mustache

ds-tidyverse

pgs_based_sample_mix-up_correction

benchmark-gwas-prio

MOLGENIS R client package

molgenis-r-client

molgenis-apps-core

Core molgenis user interface

vip-inheritance

Easily run existing MOLGENIS releases on your local machine

molgenis-cargo

VaSeBuilder

Validation Set Builder

Imputation

Repository for resource files for CAPICE and updating CAPICE model

capice-resources

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

molgenis_tools-legacy

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 Python client for the MOLGENIS REST API

molgenis-py-client

PGx-pipeline

Farmacogenetics pipeline

A MOLGENIS 'Track & Trace' dashboard for analysis pipelines

molgenis-app-pipeline-dashboard

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

ds-tidyverse-client

tsv-vcf-converter