smithlabcode repositories · GitHub

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30 repositories

falco
Public
A tool to assess the quality of sequence read data
C++
•
MIT License
•13•138•12•1•Updated Aug 28, 2026Aug 28, 2026
preseq
Public
Software for predicting library complexity and genome coverage in high-throughput sequencing.
bioinformatics sequencing capture-recapture-models
bioinformatics sequencing capture-recapture-models capture-recapture sequencing-coverage library-complexity
C++
•
GNU General Public License v3.0
•17•97•18•1•Updated Aug 26, 2026Aug 26, 2026
preseqR
Public
An R package for estimating library complexity
r sequencing r-package
r sequencing r-package capture-recapture sequencing-coverage library-complexity sequencing-library
R
•4•13•7•0•Updated Aug 25, 2026Aug 25, 2026
methbase
Public
Thousands of high-quality analyzed methylomes.
MIT License
•0•1•0•0•Updated Aug 24, 2026Aug 24, 2026
abismal
Public
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
bioinformatics bisulfite-sequencing mapping-algorithms
bioinformatics bisulfite-sequencing mapping-algorithms
C++
•
GNU General Public License v3.0
•6•20•2•0•Updated Aug 14, 2026Aug 14, 2026
dnmtools
Public
Tools for analyzing DNA methylation data
C++
•
GNU General Public License v3.0
•11•47•31•0•Updated May 18, 2026May 18, 2026
ribotricer
Public
A tool for accurately detecting actively translating ORFs from Ribo-seq data
bioinformatics translation orfs
bioinformatics translation orfs ribosome-profiling ribosome ribosome-profiling-data ribo-seq translation-regulation
Python
•
GNU General Public License v3.0
•10•43•6•0•Updated Feb 14, 2026Feb 14, 2026
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
slsa-attester
Public
SLSA Attester
MIT License
•0•0•0•0•Updated Dec 26, 2025Dec 26, 2025
bamxx
Public
HTSlib wrapper (mostly for BAM/SAM) in C++.
C++
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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
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++
•29•72•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
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-profiling riboseq differential-translation
ribosome-profiling riboseq differential-translation riborex
R
•2•12•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
translation ribosome-profiling riboseq
translation ribosome-profiling riboseq orf-detection
Jupyter Notebook
•0•9•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•21•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

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smithlabcode repositories · GitHub

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30 repositories