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arrow

Apache Arrow is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. It also provides computational libraries and zero-copy streaming messaging and interprocess communication. Languages currently supported include C, C++, Java, JavaScript, Python, and Ruby.

arrow-rs

Official Rust implementation of Apache Arrow

arrow2

transmute-free Rust library to work with the Arrow format

bat

A cat(1) clone with wings.

bb

simple process viewer in rust https://crates.io/crates/bb

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

bedtools2

A powerful toolset for genome arithmetic.

bigtools

biopython

Official git repository for Biopython (originally converted from CVS)

broot

A new way to see and navigate directory trees

bwtool

A tool for bigWig files.

bx-python-fixed-history

bx-python imported with hg-fast-export from https://bitbucket.org/james_taylor/bx-python/ with missing patched available in https://github.com/bxlab/bx-python added

cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells

cluster-buster

convert_fotorama_photobook_to_pdf

Convert flash based fotorama photobook from http://foto.com to PDF.

coreutils

Cross-platform Rust rewrite of the GNU coreutils

dragonnfruit

A method for analyzing scATAC-seq experiments.

duc

Dude, where are my bytes: Duc, a library and suite of tools for inspecting disk usage

ea-utils

Automatically exported from code.google.com/p/ea-utils

ensembl_based_rna_seq

ensembl_based_RNA_seq

extendbed

Extend/truncate intervals in BED files based on the given arguments, but keep them between the chromosome boundaries.

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

frawk

an efficient awk-like language

genomic_ranges

enomic ranges: PyRanges-like functionality using Polars dataframes instead of Pandas dataframes

hck

A sharp cut(1) clone.

iterative_peak_filtering

Iterative peak filtering.

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

moreutils-parallel

Improve parallel of moreutils (http://joeyh.name/code/moreutils/)

mrpowers-benchmarks

MrPowers benchmarks for Pandas, Dask, Vaex, Polars, Spark and Julia