Leiden University Medical Center (@LUMC)
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LUMC

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Top repositories

1

pytest-workflow

Configure workflow/pipeline tests using yaml files.
Python
63
star
2

kPAL

Analysis toolkit and programming library for k-mer profiles
Python
30
star
3

EfDS

Materials for Essentials for Data Science, a course of Statistics and Data Science master at Leiden University.
Jupyter Notebook
16
star
4

fastqsplitter

Splits fastq files evenly
Python
13
star
5

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.
PHP
12
star
6

galaxy-launcher

A project to launch the galaxy docker image easily using ansible
Ruby
11
star
7

dgeAnalysis

R package with Shiny application for DGE analysis
R
11
star
8

fastq-filter

A fast FASTQ filter program.
C
5
star
9

HAMLET

RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department
Python
5
star
10

EfDS_DB

Essentials for Data Science: 3*4h course on relational databases
Jupyter Notebook
4
star
11

rcourse

Using R for Data Analysis
R
4
star
12

CACTUS

CACTUS: Clonal Architecture of genomic Clustering of TUmor Single cells
R
4
star
13

slurm-cluster-status

Little tool for snakemake's --cluster-status argument for use with SLURM
Python
3
star
14

hutspot

Multisample DNAseq variant calling pipeline for use in diagnostics
Python
3
star
15

Nanopublication

Ruby
2
star
16

rna_cd

Detect RNA contamination in human Illumina DNA-seq experiments
Python
2
star
17

prinia

Primer design tool
Python
2
star
18

vep2lovd

Annotate, filter, and convert VEP-annotated VCFs to LOVD+ format.
Python
2
star
19

fhir-client

very basic FHIR client used send data to a FHIR-endpoint (used by github.com/LUMC/fhirhose )
Go
2
star
20

pgx-variant-tools

This library contains various methods and utilities for the calling and manipulation of normalized variants.
Python
1
star
21

array-as-vcf

Python
1
star
22

OvoGrowth-dataprocessor

Python
1
star
23

python-course

Jupyter Notebook
1
star
24

kMer

Analysis toolkit and programming library for k-mer profiles (obsoleted by kPAL)
Python
1
star
25

CACTUS-data

Data of manuscript: "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"
1
star
26

vtools

Various tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed
Python
1
star