Smith Lab

A computational biology research group at USC

smithlabcode

This organization is for code produced as a byproduct of our research in computational biology.All our repos can be found here. Our reseaerch covers diverse topics in computational genomics.So our code covers diverse topics.If you have any questions, here are several options:

Post your question as an issue in the corresponding repo.
Email the author of the code (which in most cases includes myself, Andrew).
Email me. My address is in my profile.

We release our code so it might help you. If it's not working properly or optimally,please ask us and we'll do our best to make it work for you.

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methbasemethbasePublic
Thousands of high-quality analyzed methylomes.
1
preseqpreseqPublic
Software for predicting library complexity and genome coverage in high-throughput sequencing.
C++ 82 16
falcofalcoPublic
A C++ drop-in replacement of FastQC to assess the quality of sequence read data
HTML 102 11
ribotricerribotricerPublic
A tool for accurately detecting actively translating ORFs from Ribo-seq data
Python 36 8
abismalabismalPublic
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
C++ 17 5
dnmtoolsdnmtoolsPublic
Tools for analyzing DNA methylation data
C++ 37 9

Repositories

Showing 10 of 29 repositories

abismal Public
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
smithlabcode/abismal’s past year of commit activity
C++ 17GPL-3.0 5 3 1 UpdatedFeb 20, 2025
smithlab_cpp Public
C++ code library that includes functions used in many of the Smith lab projects
smithlabcode/smithlab_cpp’s past year of commit activity
C++ 4 5 12 0 UpdatedFeb 19, 2025
bamxx Public
HTSlib wrapper (mostly for BAM/SAM) in C++.
smithlabcode/bamxx’s past year of commit activity
C++0MIT 2 0 0 UpdatedFeb 14, 2025
dnmtools Public
Tools for analyzing DNA methylation data
smithlabcode/dnmtools’s past year of commit activity
C++ 37GPL-3.0 9 28 (1 issue needs help) 0 UpdatedFeb 11, 2025
ribotricer Public
A tool for accurately detecting actively translating ORFs from Ribo-seq data
smithlabcode/ribotricer’s past year of commit activity
Python 36GPL-3.0 8 4 0 UpdatedJan 30, 2025
methbase Public
Thousands of high-quality analyzed methylomes.
smithlabcode/methbase’s past year of commit activity
1MIT0 0 0 UpdatedNov 25, 2024
falco Public
A C++ drop-in replacement of FastQC to assess the quality of sequence read data
smithlabcode/falco’s past year of commit activity
HTML 102GPL-3.0 11 20 (1 issue needs help) 0 UpdatedNov 22, 2024
preseq Public
Software for predicting library complexity and genome coverage in high-throughput sequencing.
smithlabcode/preseq’s past year of commit activity
C++ 82GPL-3.0 16 17 0 UpdatedOct 21, 2024
cread Public
Software tools for regulatory sequence analysis
smithlabcode/cread’s past year of commit activity
C++0GPL-3.00 0 0 UpdatedNov 29, 2023
sperm-methylome-aging-wgbs Public
Scripts, pipelines, summary data and figures for this project.
smithlabcode/sperm-methylome-aging-wgbs’s past year of commit activity
R0GPL-3.00 0 0 UpdatedMar 20, 2023