LUMC/hutspot

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Language
Python
License
GNU Affero Genera...
Created over 5 years ago
Updated almost 3 years ago

LUMC/hutspot

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Multisample DNAseq variant calling pipeline for use in diagnostics

pytest-workflow

Configure workflow/pipeline tests using yaml files.

kPAL

Analysis toolkit and programming library for k-mer profiles

EfDS

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

Jupyter Notebook

fastqsplitter

Splits fastq files evenly

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.

galaxy-launcher

A project to launch the galaxy docker image easily using ansible

dgeAnalysis

R package with Shiny application for DGE analysis

fastq-filter

A fast FASTQ filter program.

HAMLET

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

EfDS_DB

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

Jupyter Notebook

rcourse

Using R for Data Analysis

CACTUS

CACTUS: Clonal Architecture of genomic Clustering of TUmor Single cells

slurm-cluster-status

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

Nanopublication

rna_cd

Detect RNA contamination in human Illumina DNA-seq experiments

prinia

Primer design tool

vep2lovd

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

fhir-client

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

pgx-variant-tools

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

array-as-vcf

OvoGrowth-dataprocessor

python-course

Jupyter Notebook

kMer

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

CACTUS-data

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

vtools

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