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    30 repositories

    • smithlab_cpp

      Public
      C++ code library that includes functions used in many of the Smith lab projects
      C++
      •5•4•12•0•Updated Jan 6, 2026Jan 6, 2026

    • abismal

      Public
      Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
      bioinformaticsbisulfite-sequencingmapping-algorithms
      C++
      •
      GNU General Public License v3.0
      •5•20•0•0•Updated Jan 6, 2026Jan 6, 2026

    • methbase

      Public
      Thousands of high-quality analyzed methylomes.
      MIT License
      •0•1•0•0•Updated Jan 5, 2026Jan 5, 2026

    • dnmtools

      Public
      Tools for analyzing DNA methylation data
      C++
      •
      GNU General Public License v3.0
      •11•44•32•0•Updated Jan 1, 2026Jan 1, 2026

    • slsa-attester

      Public
      SLSA Attester
      MIT License
      •0•0•0•0•Updated Dec 26, 2025Dec 26, 2025

    • preseq

      Public
      Software for predicting library complexity and genome coverage in high-throughput sequencing.
      bioinformaticssequencingcapture-recapture-modelscapture-recapturesequencing-coveragelibrary-complexity
      C++
      •
      GNU General Public License v3.0
      •17•92•18•1•Updated Dec 24, 2025Dec 24, 2025

    • bamxx

      Public
      HTSlib wrapper (mostly for BAM/SAM) in C++.
      C++
      •
      MIT License
      •2•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • rseg

      Public
      A software tool to identify dispersed epigenetic regions from ChIP-seq data
      C
      •0•7•7•0•Updated Nov 13, 2025Nov 13, 2025

    • dme

      Public
      The DME algorithm for discovering motifs that distinguish two sets of sequences.
      C++
      •0•0•0•0•Updated Oct 30, 2025Oct 30, 2025

    • falco

      Public
      A C++ drop-in replacement of FastQC to assess the quality of sequence read data
      HTML
      •
      GNU General Public License v3.0
      •12•123•16•0•Updated Aug 11, 2025Aug 11, 2025

    • ribotricer

      Public
      A tool for accurately detecting actively translating ORFs from Ribo-seq data
      bioinformaticstranslationorfsribosome-profilingribosomeribosome-profiling-dataribo-seqtranslation-regulation
      Python
      •
      GNU General Public License v3.0
      •9•39•6•0•Updated Jan 30, 2025Jan 30, 2025

    • cread

      Public
      Software tools for regulatory sequence analysis
      C++
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 29, 2023Nov 29, 2023

    • sperm-methylome-aging-wgbs

      Public
      Scripts, pipelines, summary data and figures for this project.
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 20, 2023Mar 20, 2023

    • methpipe

      Public archive
      A pipeline for analyzing DNA methylation data from bisulfite sequencing.
      C++
      •28•71•0•0•Updated Oct 7, 2022Oct 7, 2022

    • .github

      Public
      The base repo for the smithlabcode organization
      0•0•0•0•Updated Sep 15, 2022Sep 15, 2022

    • preseqR

      Public
      An R package for estimating library complexity
      rsequencingr-packagecapture-recapturesequencing-coveragelibrary-complexitysequencing-library
      R
      •4•13•6•0•Updated Sep 4, 2022Sep 4, 2022

    • walt

      Public archive
      WALT is a read mapping program for bisulfite sequencing DNA methylation studies.
      C++
      •
      GNU General Public License v3.0
      •8•17•9•0•Updated Aug 23, 2022Aug 23, 2022

    • riborex

      Public
      Riborex: Fast and flexible identification of differential translation from Ribo-seq data
      ribosome-profilingriboseqdifferential-translationriborex
      R
      •2•11•3•0•Updated Apr 9, 2021Apr 9, 2021

    • ribotricer-results

      Public
      Results and scripts for benchmarking ribotricer for translating ORF detection from Ribo-seq data
      translationribosome-profilingriboseqorf-detection
      Jupyter Notebook
      •0•8•0•0•Updated Jan 8, 2021Jan 8, 2021

    • utils

      Public
      A collection of utility programs that might be useful to someone.
      C++
      •0•1•1•0•Updated Sep 20, 2020Sep 20, 2020

    • epievo

      Public
      Programs for simulating and inferring epigenome evolution.
      C++
      •
      GNU General Public License v3.0
      •1•1•5•0•Updated Jun 15, 2020Jun 15, 2020

    • smurfseq_scripts

      Public
      Scripts and some documentation for how we did CNV analysis using SMURF-seq reads and how we generated simulated data to evaluate mapping performance.
      Python
      •
      GNU General Public License v3.0
      •1•4•0•0•Updated Jun 17, 2019Jun 17, 2019

    • amordad

      Public
      Amordad is a database engine for high dimensional data
      C++
      •
      GNU General Public License v3.0
      •0•3•1•0•Updated Jan 13, 2019Jan 13, 2019

    • piranha

      Public
      Piranha is a peak-caller for CLIP- and RIP-seq data
      C++
      •16•20•15•0•Updated Feb 7, 2018Feb 7, 2018

    • Epiphyte

      Public
      A package for estimating phylogenetic tree for epigenomes (DNA methylation primarily) from multiple species.
      C++
      •
      GNU General Public License v3.0
      •3•5•1•0•Updated Feb 5, 2018Feb 5, 2018

    • mlml

      Public archive
      Simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels
      C++
      •2•3•0•0•Updated Feb 4, 2018Feb 4, 2018

    • -DEPRECATED-amrfinder

      Public
      DEPRECATED: ACTIVELY MANAGED SOFTWARE IN METHPIPE REPOSITORY.
      C++
      •1•0•1•0•Updated Apr 12, 2016Apr 12, 2016

    • rmap

      Public
      Short reads mapper for next-generation sequencing data (DNA-seq, BS-seq, etc)
      C++
      •2•5•4•0•Updated Jul 21, 2015Jul 21, 2015

    • zagros

      Public
      Zagros is an algorithm for motif discovery in CLIP-seq data
      C++
      •0•2•7•0•Updated Nov 4, 2014Nov 4, 2014

    • radmeth

      Public
      C++
      •
      GNU General Public License v3.0
      •2•3•1•0•Updated May 1, 2014May 1, 2014