Pinned Repositories
bankers2
A set of tools to create plotting files from subset counts in banker's sequenc order. I.e. helper scripts for the visualisation of count data across all possible subsets of a sample set.
bcftools
This is my own personal development repository for BCFtools. Check out the main repository at: https://github.com/samtools/bcftools
bioconda-recipes
Conda recipes for the bioconda channel.
bioconda-utils
Utilities for building and managing bioconda recipes
cargo
The Rust package manager
rna-seq-kallisto-sleuth
A workflow for RNA-seq differential expression analysis based on Kallisto and Sleuth.
TutMinicondaSnakemake
dlaehnemann's Repositories
dlaehnemann/rna-seq-kallisto-sleuth
A workflow for RNA-seq differential expression analysis based on Kallisto and Sleuth.
dlaehnemann/bioconda-recipes
Conda recipes for the bioconda channel.
dlaehnemann/coin-or-cbc-feedstock
A conda-smithy repository for coin-or-cbc.
dlaehnemann/coin_cbc
Rust bindings to the CoinOR CBC MILP Solveur using the C API.
dlaehnemann/coincbc-feedstock
A conda-smithy repository for coincbc.
dlaehnemann/create-ecdna-testing-data
create long read (Nanopore with NanoSim) and short read (Illumina with Circle-Map) testing data for ecDNA analysis workflows
dlaehnemann/create-quant-seq-testing-dataset
A Snakemake workflow for (reproducibly) creating a QuantSeq 3' mRNA testing dataset that is both small enough to run in standard continuous integration testing environments, and large enough to produce (some reasonably) meaningful results.
dlaehnemann/create-sv-ci-testing-dataset
a mini snakemake workflow to produce structural variant testing dataset small enough for CI systems, but large enough to be meaningful
dlaehnemann/datavzrd
A tool to create visual HTML reports from collections of CSV/TSV tables
dlaehnemann/deepTools
Tools to process and analyze deep sequencing data.
dlaehnemann/demo-standardized-workflow
dlaehnemann/evaluate_varlociraptor_purity_estimation
A little snakemake workflow to evaluate the varlociraptor subcommand `estimate contamination`.
dlaehnemann/hopr
This is the development site for Hands-On Programming with R, a book that teaches how to program in R, with hands-on examples. Read the book at https://rstudio-education.github.io/hopr.
dlaehnemann/lsf
Snakemake profile for running jobs on an LSF cluster
dlaehnemann/media
Various media related scripts
dlaehnemann/Microarrays-R
dlaehnemann/NanoSim
Nanopore sequence read simulator
dlaehnemann/neofox
Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors
dlaehnemann/prosic2
Version 2 of the PROSIC caller for somatic variants.
dlaehnemann/r4ds
R for data science: a book
dlaehnemann/rna-seq-conservative-fold-change-without-replicates
snakemake workflow to determine conservative fold changes between transcriptomic samples when no biological replicates are available
dlaehnemann/rust-lp-modeler
Lp modeler written in Rust
dlaehnemann/rust-script-feedstock
A conda-smithy repository for rust-script.
dlaehnemann/SCIPhI
dlaehnemann/scVILP
dlaehnemann/sleuth
Differential analysis of RNA-Seq
dlaehnemann/slurm-cluster-in-github-actions
Using OSD slurm-bundle to set up a slurm cluster in GitHub Actions via juju.
dlaehnemann/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
dlaehnemann/snakemake-executor-plugin-lsf
A Snakemake executor plugin for submitting jobs to a LSF cluster
dlaehnemann/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks