Christian Brueffer's Projects
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Fit data to many distributions
a lightweight db framework for disease and population genetics.
Genome data visualizations
'ggplot2' Based Publication Ready Plots
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Community Documentation for the Carpentries
Graph-based alignment (Hierarchical Graph FM index)
:ramen: Minimalist Jekyll Template
The Journal of Open Source Software
Fast and accurate coordinate conversion between assemblies
The libxo library allows an application to generate text, XML, JSON, and HTML output using a common set of function calls. The application decides at run time which output style should be produced.
matplotlib: plotting with Python
Repository for miscellaneous bioinformatics scripts that may be useful to others.
R Shiny based lightweight mutation exploration tool
Fork of the Numpy main repository
OpenBSM open audit implementation
pamr — Pam: prediction analysis for microarrays
Git pre-commit hook that checks for Python PEP8 style compliance.
LaTeX sources for my PhD thesis RNA Sequencing for Molecular Diagnostics in Breast Cancer at the Lund University Faculty of Medicine (published December 2020).
Scripts to generate plots for my PhD thesis.
OPNsense plugin collection
Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
A conda-smithy repository for r.
A conda-smithy repository for r-xml.
RStudio is an integrated development environment (IDE) for R
Plot structural variant signals from many BAMs and CRAMs
This is the official development repository for samtools.