andrewdavidsmith

adssrc

A subset of the programs I use in my own data analysis.

adapto-rs

Remove adaptors from short-read bisulfite sequencing data (coded in rust)

adapto-rs-teaching

abismal

Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

bioconda-recipes

Conda recipes for the bioconda channel.

dnmtools

Tools for analyzing DNA methylation data

falco

A C++ drop-in replacement of FastQC to assess the quality of sequence read data

libz-sys

Rust crate package to link to a system libz (zlib)

mcounts

Implementation of count from dnmtools in rust

mlevels

Implementation of the levels command from dnmtools in rust

msite

Implementation of msite in rust

msym

Make sites symmetric CpGs in counts format DNA methylation levels

preseqR

An R package for estimating library complexity

pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

qbio578a-examples

I'm using this repo to share some code I use for demonstrating algorithms

radmeth-demo-simulated-data

Simulated data that was used to generate part of the documentation for radmeth

rsegwork

rsegwork