A lua package for designing DNA.

Base frequencies for BAM files

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

PYTHIA files for simulating pp collisions at LHC energies with pileup

Convert output from Samtools pileup into a matrix.

Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).

A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.

📦 Pile up cardboard boxes 📦

Variant caller from pileup notation / samtools alignment

Get the consensus sequences from SAM (and BAM) files, ignoring the reference

Parse pileup files, generate consensus fasta and calculate heteroplasmy per nucleotide