Gert Hulselmans's repositories
arrow-rs
Official Rust implementation of Apache Arrow
bcftools
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
biobear
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
biopython
Official git repository for Biopython (originally converted from CVS)
cellsnp-lite
Efficient genotyping bi-allelic SNPs on single cells
coreutils
Cross-platform Rust rewrite of the GNU coreutils
dragonnfruit
A method for analyzing scATAC-seq experiments.
exon
Exon is an OLAP query engine specifically for biology and life science applications.
genomic_ranges
enomic ranges: PyRanges-like functionality using Polars dataframes instead of Pandas dataframes
hck
A sharp cut(1) clone.
jefscheepers_toolbox
A variety of tools for my own use
lda
Topic modeling with latent Dirichlet allocation using Gibbs sampling
maturin
Build and publish crates with pyo3, rust-cpython and cffi bindings as well as rust binaries as python packages
mrpowers-benchmarks
MrPowers benchmarks for Pandas, Dask, Vaex, Polars, Spark and Julia
noodles
Bioinformatics I/O libraries in Rust
oxbow
Read specialized NGS formats as data frames in R, Python, and more.
plda
PLDA: Parallel Latent Dirichlet Allocation in C++
polars-book
Book documentation of the Polars DataFrame library
polars-feedstock
A conda-smithy repository for polars.
pyfasta
fast, memory-efficient, pythonic (and command-line) access to fasta sequence files
pyo3
Rust bindings for the Python interpreter
rustybam
bioinformatics toolkit in rust
TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
vireo
Demultiplexing pooled scRNA-seq data with or without genotype reference
vmtouch
Portable file system cache diagnostics and control