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DEPRECATED: ACTIVELY MANAGED SOFTWARE IN METHPIPE REPOSITORY.

.github

The base repo for the smithlabcode organization

abismal

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

amordad

Amordad is a database engine for high dimensional data

bamxx

HTSlib wrapper (mostly for BAM/SAM) in C++.

cread

Software tools for regulatory sequence analysis

dme

The DME algorithm for discovering motifs that distinguish two sets of sequences.

dnmtools

Tools for analyzing DNA methylation data

epievo

Programs for simulating and inferring epigenome evolution.

epiphyte

A package for estimating phylogenetic tree for epigenomes (DNA methylation primarily) from multiple species.

falco

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

methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.

mlml

Simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels

piranha

Piranha is a peak-caller for CLIP- and RIP-seq data

preseq

Software for predicting library complexity and genome coverage in high-throughput sequencing.

preseqr

An R package for estimating library complexity

radmeth

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

ribotricer-results

Results and scripts for benchmarking ribotricer for translating ORF detection from Ribo-seq data

rmap

Short reads mapper for next-generation sequencing data (DNA-seq, BS-seq, etc)

rseg

A software tool to identify dispersed epigenetic regions from ChIP-seq data

smithlab_cpp

C++ code library that includes functions used in many of the Smith lab projects

smurfseq_scripts

Scripts and some documentation for how we did CNV analysis using SMURF-seq reads and how we generated simulated data to evaluate mapping performance.

sperm-methylome-aging-wgbs

Scripts, pipelines, summary data and figures for this project.

utils

A collection of utility programs that might be useful to someone.

walt

WALT is a read mapping program for bisulfite sequencing DNA methylation studies.

zagros

Zagros is an algorithm for motif discovery in CLIP-seq data