LUMC/EfDS

Materials for Essentials for Data Science, a course of Statistics and Data Science master at Leiden University.

Language: Jupyter Notebook - Size: 19.1 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 15 - Forks: 29

LUMC/pytest-workflow

Configure workflow/pipeline tests using yaml files.

Language: Python - Size: 756 KB - Last synced: 25 days ago - Pushed: about 2 months ago - Stars: 63 - Forks: 8

LUMC/kPAL

Analysis toolkit and programming library for k-mer profiles

Language: Python - Size: 361 KB - Last synced: 3 days ago - Pushed: about 3 years ago - Stars: 30 - Forks: 6

LUMC/fastqsplitter

Splits fastq files evenly

Language: Python - Size: 396 KB - Last synced: about 11 hours ago - Pushed: almost 4 years ago - Stars: 16 - Forks: 7

LUMC/HAMLET

RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department

Language: Python - Size: 26.9 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 3

LUMC/wg-app-template

Language: JavaScript - Size: 351 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

LUMC/wg-app-ovogrowth

Language: JavaScript - Size: 36.1 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

LUMC/vep2lovd

Annotate, filter, and convert VEP-annotated VCFs to LOVD+ format.

Language: Python - Size: 91.8 KB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

LUMC/miniwdl-slurm 📦

Extends miniwdl to run workflows on SLURM clusters in singularity containers.

Language: Python - Size: 40 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

LUMC/pigz-container

Docker container based on Debian buster containing pigz

Language: Dockerfile - Size: 1000 Bytes - Last synced: about 2 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

LUMC/KeyGenes-dataprocessor

Language: Python - Size: 6.6 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

LUMC/PacBio-merge

Merge report files from PacBio tools

Language: Python - Size: 19.5 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

LUMC/python-course

Language: Jupyter Notebook - Size: 36.9 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 5

LUMC/SSLP-Analyzer

Language: PHP - Size: 557 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

LUMC/freebayes-snakemake

Short read pipeline using bwa-mem2, freebayes and whatshap to call phased variants

Language: Python - Size: 980 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

LUMC/git-synchronizer

A python program that will mirror git repos by automated push pulling

Language: Python - Size: 60.5 KB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

LUMC/django Fork of django/django

The Web framework for perfectionists with deadlines.

Language: Python - Size: 54.8 MB - Last synced: about 2 months ago - Pushed: almost 11 years ago - Stars: 0 - Forks: 0

LUMC/bioconda-recipes Fork of bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

Language: Shell - Size: 147 MB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

LUMC/vtools

Various tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed

Language: Python - Size: 204 KB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 1

LUMC/prinia

Primer design tool

Language: Python - Size: 66.4 KB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 1

LUMC/wg-app-keygenes

Language: JavaScript - Size: 18.9 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

LUMC/Nanopublication

Language: Ruby - Size: 201 KB - Last synced: about 2 months ago - Pushed: over 11 years ago - Stars: 2 - Forks: 3

LUMC/MultiQC_PGx

MultiQC plugin for the LUMC PGx project

Language: Python - Size: 34.2 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

LUMC/slurm-cluster-status

Little tool for snakemake's --cluster-status argument for use with SLURM

Language: Python - Size: 7.81 KB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 3 - Forks: 2

LUMC/webapp-gen-system

Language: TSQL - Size: 43.7 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

LUMC/lumc-galaxy-tools

Tools developed for use on LUMC's galaxy instance

Language: Python - Size: 1.07 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

LUMC/sentinel

JSON-based QC database for NGS statistics

Language: Scala - Size: 2.61 MB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

LUMC/singularity-recipes

Recipes for singularity containers used by LUMC analysis pipelines

Size: 1000 Bytes - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

LUMC/hutspot

Multisample DNAseq variant calling pipeline for use in diagnostics

Language: Python - Size: 5.98 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 2

LUMC/docker_ubuntu_gridengine_drmaa Fork of bow/docker_ubuntu_drmaa_conda

For building a docker image on Ubuntu with Grid Engine, DRMAA, and miniconda installed.

Language: Shell - Size: 76.2 KB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

LUMC/haploblock-combiner

Generate all possible combinations between phased haploblocks

Language: Python - Size: 88.9 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

LUMC/gitlabhq Fork of gitlabhq/gitlabhq

Project management and code hosting application. Follow us on twitter @gitlabhq

Language: Ruby - Size: 224 MB - Last synced: about 2 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

LUMC/MRN-browser

Language: HTML - Size: 1.34 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

LUMC/galaxy-launcher

A project to launch the galaxy docker image easily using ansible

Language: Ruby - Size: 1020 KB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 11 - Forks: 4

LUMC/gene-coverage

A program to calculate coverage per feature over one or more samples.

Size: 881 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

LUMC/CACTUS-data

Data of manuscript: "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"

Size: 17.8 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

LUMC/EfDS_DB

Essentials for Data Science: 3*4h course on relational databases

Language: Jupyter Notebook - Size: 5.93 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 3 - Forks: 12

LUMC/Argalaxy-ImmuneRepertoire Fork of ErasmusMC-Bioinformatics/Argalaxy-ImmuneRepertoire

Argalaxy Immune Repertoire pipeline

Language: R - Size: 4.35 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

LUMC/docker-galaxy-compose

A basic galaxy container for docker-compose setups. Includes a conda installation.

Language: Dockerfile - Size: 37.1 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1

LUMC/docker-pysam-tqdm-debian

Container with pysam, tqdm on python 3.7 on debian stretch

Language: Dockerfile - Size: 0 Bytes - Last synced: about 2 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

LUMC/django-fsm Fork of viewflow/django-fsm

Django friendly finite state machine support

Language: Python - Size: 132 KB - Last synced: about 2 months ago - Pushed: over 11 years ago - Stars: 0 - Forks: 0

LUMC/gnomad-merge

Snakemake pipeline to merge gnomAD VCF files

Language: Python - Size: 59.6 KB - Last synced: about 2 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

LUMC/directus-manager

Language: Python - Size: 25.4 KB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

LUMC/array-as-vcf

Language: Python - Size: 182 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

LUMC/ansible-role-xwiki-docker

Ansible role for setting up an xwiki instance that is powered by a docker stack.

Language: Shell - Size: 32.2 KB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

LUMC/docker-singularity-snakemake

Docker image based on debian:buster that includes both singularity version 3 and snakemake 5.4

Language: Dockerfile - Size: 5.86 KB - Last synced: about 2 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

LUMC/ansible-role-galaxy_docker

Language: Python - Size: 77.1 KB - Last synced: about 2 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

LUMC/ansible-galaxy-cluster

Ansible role for installing galaxy on a node connected to a cluster.

Language: Jinja - Size: 56.6 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

LUMC/dgeAnalysis

R package with Shiny application for DGE analysis

Language: R - Size: 36.6 MB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 11 - Forks: 5

LUMC/docker-galaxy-uwsgi

Language: Dockerfile - Size: 52.7 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

LUMC/vcfphasesets

Get variants as phase sets from a VCF file using pysam.

Language: Python - Size: 6.84 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

LUMC/rna_cd

Detect RNA contamination in human Illumina DNA-seq experiments

Language: Python - Size: 1.34 MB - Last synced: 6 days ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 0

LUMC/PacBio-variantcalling

Variant calling workflow for PacBio HiFi data. Part of the LUMC PGx project.

Language: wdl - Size: 193 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

LUMC/ribosome-profiling-analysis-framework

Ribosome profiling analysis framework as described in de Klerk E., Fokkema I.F.A.C et al (2015). Alignment, triplet periodicity analysis, detecting ORFs.

Language: PHP - Size: 3.8 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 12 - Forks: 6

LUMC/RPCA Fork of bayraktar1/RPCA

RNA-seq pipeline comparison and analyses

Language: Python - Size: 2.62 MB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

LUMC/rcourse

Using R for Data Analysis

Language: R - Size: 385 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 1

LUMC/OvoGrowth-dataprocessor

Language: Python - Size: 123 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

LUMC/fastq-filter

A fast FASTQ filter program.

Language: C - Size: 253 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 5 - Forks: 3

LUMC/FAIRDataPoint Fork of FAIRDataTeam/FAIRDataPoint

Fork of the FAIR Data Point repository, collecting changes and issues with the FDP implementation at the LUMC.

Size: 11.6 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

LUMC/CACTUS

CACTUS: Clonal Architecture of genomic Clustering of TUmor Single cells

Language: R - Size: 17.9 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 4 - Forks: 0

LUMC/shm_csr Fork of ErasmusMC-Bioinformatics/shm_csr

Somatic hypermutation and class switch recombination pipeline

Language: R - Size: 4.5 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 1

LUMC/w3id.org Fork of perma-id/w3id.org

Website source code for w3id.org.

Language: HTML - Size: 5.82 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

LUMC/fhir-client

very basic FHIR client used send data to a FHIR-endpoint (used by github.com/LUMC/fhirhose )

Language: Go - Size: 510 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 1

LUMC/fhirhose

Language: Go - Size: 36.1 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

LUMC/pgx-variant-tools

This library contains various methods and utilities for the calling and manipulation of normalized variants.

Language: Python - Size: 43 KB - Last synced: 21 days ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

LUMC/pgx-pipe-helper

Utility module to provide consistent handling of barcodes and loci by the PGx pipeline stages.

Language: Python - Size: 6.84 KB - Last synced: 28 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

LUMC/locus_processing

Methods and tools for processing locus definition files.

Language: Python - Size: 24.4 KB - Last synced: 19 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

LUMC/kMer

Analysis toolkit and programming library for k-mer profiles (obsoleted by kPAL)

Language: Python - Size: 609 KB - Last synced: about 2 months ago - Pushed: over 9 years ago - Stars: 1 - Forks: 0