Devon Ryan

ChromosomeMappings. This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

MethylDackel. A (mostly) universal methylation extractor for BS-seq experiments.

libBigWig. A C library for handling bigWig files

SE-MEI. Tools for finding mobile element insertions from single-end datasets

MethIndelRealigner. A local realigner around InDels for MethylSeq data

Misc. Misc. utilities

bison. Bisulfite alignment on nodes of a cluster

Answers. Random code produced to answer questions on biostars/seqanswers/etc.

libGTF. A library for processing and searching GTF and BED files

lib2bit. A C library for accessing 2bit files

BBMeth. BBMeth: An R package for fitting methylation data with a beta-binomial model

tetoolkit. A package for including transposable elements in differential enrichment analysis of sequencing datasets.

pyBigWig. A python extension for quick access to bigWig and bigBed files

bwa-meth. align BS-Seq reads and extract methylation without intermediate temp files

HTCondor-galaxy. A docker container for layering HTCondor on top of a Galaxy docker image

RNAcentralTools. A set of tools useful for using RNAcentral in smallRNAseq analyses.

MultiQC. Aggregate results from bioinformatics analyses across many samples into a single report.