Pinned Repositories
abismal
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
adapto-rs
Remove adaptors from short-read bisulfite sequencing data (coded in rust)
adapto-rs-teaching
adssrc
A subset of the programs I use in my own data analysis.
abismal
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
dnmtools
Tools for analyzing DNA methylation data
falco
A C++ drop-in replacement of FastQC to assess the quality of sequence read data
preseq
Software for predicting library complexity and genome coverage in high-throughput sequencing.
riborex
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
ribotricer
A tool for accurately detecting actively translating ORFs from Ribo-seq data
andrewdavidsmith's Repositories
andrewdavidsmith/adssrc
A subset of the programs I use in my own data analysis.
andrewdavidsmith/abismal
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
andrewdavidsmith/adapto-rs
Remove adaptors from short-read bisulfite sequencing data (coded in rust)
andrewdavidsmith/adapto-rs-teaching
andrewdavidsmith/bioconda-recipes
Conda recipes for the bioconda channel.
andrewdavidsmith/dnmtools
Tools for analyzing DNA methylation data
andrewdavidsmith/falco
A C++ drop-in replacement of FastQC to assess the quality of sequence read data
andrewdavidsmith/libz-sys
Rust crate package to link to a system libz (zlib)
andrewdavidsmith/mcounts
Implementation of count from dnmtools in rust
andrewdavidsmith/mlevels
Implementation of the levels command from dnmtools in rust
andrewdavidsmith/msite
Implementation of msite in rust
andrewdavidsmith/msym
Make sites symmetric CpGs in counts format DNA methylation levels
andrewdavidsmith/mxe
Methylome transfer engine (mxe)
andrewdavidsmith/preseqR
An R package for estimating library complexity
andrewdavidsmith/pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
andrewdavidsmith/qbio578a-examples
I'm using this repo to share some code I use for demonstrating algorithms
andrewdavidsmith/radmeth-demo-simulated-data
Simulated data that was used to generate part of the documentation for radmeth
andrewdavidsmith/rsegwork
rsegwork