Pinned Repositories
calfreeslots
A small command line utility for printing free calendar slots in the coming days
conda-inject
Helper functions for injecting a conda environment into the current python environment (by modifying sys.path, without actually changing the current python environment)
data-science-for-bioinfo
A collection of resources for data scientists (not only) in bioinformatics
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
fp-rust-wavelet-trees
locosopa
A github action for creating software homepages with low code.
microphaser
nanopore-qc
A quality control pipeline for Oxford Nanopore sequencing
setup-slurm-action
A github action to setup a small SLURM cluster for testing purposes.
srptn
SeRPentine - the Snakemake research platform
Bioinformatics and Computational Oncology (Koesterlab)'s Repositories
koesterlab/microphaser
koesterlab/setup-slurm-action
A github action to setup a small SLURM cluster for testing purposes.
koesterlab/fp-rust-wavelet-trees
koesterlab/calfreeslots
A small command line utility for printing free calendar slots in the coming days
koesterlab/data-science-for-bioinfo
A collection of resources for data scientists (not only) in bioinformatics
koesterlab/dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
koesterlab/conda-inject
Helper functions for injecting a conda environment into the current python environment (by modifying sys.path, without actually changing the current python environment)
koesterlab/locosopa
A github action for creating software homepages with low code.
koesterlab/ngs-fastq-to-cram
Snakemake workflow for converting FASTQ files to self-contained CRAM files with maximum lossless compression.
koesterlab/srptn
SeRPentine - the Snakemake research platform
koesterlab/Feature-extraction-from-random-forest
A repo to extract imporant features and its associated features from a random forest
koesterlab/autoref
A snakemake workflow for downloading reference data from, e.g. aws-igenomes
koesterlab/chm-synthetic-tumor-normal
Creating a synthetic tumor/normal sample pair from CHM1/CHM13 haploid cell lines.
koesterlab/datavzrd-chatbot
A chatbot to create datavzrd configs
koesterlab/fgbio
Tools for working with genomic and high throughput sequencing data.
koesterlab/genomes
web-based genome viewer
koesterlab/go_term_p_value_aggregation
Code to aggregate sleuth differential expression p-values of individual transcripts to GO terms. (WIP!)
koesterlab/HLA-simulation-evaluation
koesterlab/koesterlab-workstation-ansible
koesterlab/koesterlab.github.io
koesterlab/ngs-test-data
A workflow for creating small NGS test data sets, useful for continuous integration.
koesterlab/praxisprojekt-rust-ss-2024
koesterlab/remail
koesterlab/rna-seq-kallisto-sleuth
koesterlab/rossi-ips-dmr
Calling and plotting of differentially methylated regions between two or more biological samples in BAM format
koesterlab/single-cell-rna-seq
A single cell RNA-seq workflow following http://dx.doi.org/10.12688/f1000research.9501.2
koesterlab/snakemake-gitpod-template
A gitpod template for developing a Snakemake workflow
koesterlab/teaching-data-analysis-visualization-reproducibility
Course on data analysis, visualization and reproducibility at the faculty of medicine
koesterlab/texp
koesterlab/voyager
Visualization Tool for Data Exploration