pyrle

Last released Dec 14, 2023

Numeric run length encoding for Python.

poranges

Last released Jun 30, 2023

pyranges

Last released Jun 29, 2023

GenomicRanges for Python.

sorted-nearest

Last released May 19, 2023

Find nearest intervals.

bwread

Last released May 18, 2023

Read bigwig files into Python data science formats.

ncls

Last released May 18, 2023

A fast interval tree-like implementation in C, wrapped for the Python ecosystem.

bamread

Last released May 17, 2023

Read bam files quickly into dataframes in Python

epic2

Last released Sep 5, 2021

Ultraperformant ChIP-Seq broad peak/domain finder.

pyranges-db

Last released Feb 3, 2020

Database add-on for PyRanges.

piedpiper

Last released Apr 15, 2019

Debug context manager for chained commands.

bioepic

Last released Aug 2, 2018

Chip-Seq broad peak/domain finder.

sphinx-autorun-ebs

Last released May 16, 2018

Sphinx extension autorun

clustertree

Last released May 14, 2018

Clustertrees.

kerneltree

Last released May 4, 2018

Ultrafast interval tree implementation.

kg

Last released Dec 1, 2017

Access KEGG from the command line.

snpflip

Last released Dec 1, 2017

Report reverse and ambiguous strand SNPs.

hdose

Last released Oct 30, 2017

Harmonize exposure, outcome and dosage for Mendelian Randomization.

triform2

Last released Sep 6, 2016

Improved sensitivity, specificity and control of false discovery rates in ChIP-Seq peak finding.

ebs

Last released Apr 20, 2016

Various utils I use in more than one script/lib

goverlap

Last released Nov 26, 2015

Powerful ontology term enrichment analyzer for the command line

biomartian

Last released Nov 24, 2015

Access BioMart from the command line.

godb

Last released Oct 20, 2015

A set of annotation maps describing most of the Gene Ontology.

widediaper

Last released Sep 29, 2015

Simple, stable, easily debuggable R/Python piping