A pipeline for analyzing DNA methylation data from bisulfite sequencing.
C++ code library that includes functions used in many of the Smith lab projects
WALT is a read mapping program for bisulfite sequencing DNA methylation studies.
The DME algorithm for discovering motifs that distinguish two sets of sequences.
Software for predicting library complexity and genome coverage in high-throughput sequencing.
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
A software tool to identify dispersed epigenetic regions from ChIP-seq data
DEPRECATED: ACTIVELY MANAGED SOFTWARE IN METHPIPE REPOSITORY.
Short reads mapper for next-generation sequencing data (DNA-seq, BS-seq, etc)
Amordad is a database engine for high dimensional data
Piranha is a peak-caller for CLIP- and RIP-seq data
Zagros is an algorithm for motif discovery in CLIP-seq data
Simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels