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@smithlabcode

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.

Pinned

  1. methpipe methpipe Public archive

    A pipeline for analyzing DNA methylation data from bisulfite sequencing.

    C++ 66 28

  2. preseq preseq Public

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

    C++ 75 15

  3. falco falco Public

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

    HTML 89 10

  4. ribotricer ribotricer Public

    A tool for accurately detecting actively translating ORFs from Ribo-seq data

    Python 28 8

  5. abismal abismal Public

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

    C++ 11 4

  6. dnmtools dnmtools Public

    Tools for analyzing DNA methylation data

    C++ 22 7

Repositories

Showing 10 of 29 repositories
  • methbase Public

    Thousands of high-quality analyzed methylomes.

    smithlabcode/methbase’s past year of commit activity
    0 MIT 0 0 0 Updated Jun 19, 2024
  • dnmtools Public

    Tools for analyzing DNA methylation data

    smithlabcode/dnmtools’s past year of commit activity
    C++ 22 GPL-3.0 7 23 (1 issue needs help) 0 Updated Jun 17, 2024
  • 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 Updated Jun 9, 2024
  • 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++ 11 GPL-3.0 4 2 0 Updated Jun 8, 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 89 GPL-3.0 10 16 (1 issue needs help) 0 Updated Jun 2, 2024
  • ribotricer Public

    A tool for accurately detecting actively translating ORFs from Ribo-seq data

    smithlabcode/ribotricer’s past year of commit activity
    Python 28 GPL-3.0 8 4 0 Updated Apr 13, 2024
  • bamxx Public

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

    smithlabcode/bamxx’s past year of commit activity
    C++ 0 MIT 2 0 0 Updated Dec 9, 2023
  • cread Public

    Software tools for regulatory sequence analysis

    smithlabcode/cread’s past year of commit activity
    C++ 0 GPL-3.0 0 0 0 Updated Nov 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
    R 0 GPL-3.0 0 0 0 Updated Mar 20, 2023
  • preseq Public

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

    smithlabcode/preseq’s past year of commit activity
    C++ 75 GPL-3.0 15 16 0 Updated Oct 18, 2022