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@stajichlab

Jason Stajich Lab at UC Riverside

Evolutionary Genomics of Fungi projects, data and software
README.md

These repositories for the Stajich laboratory at UC Riverside focused on Genomics, Bioinformatics, Evolution of (mostly) Fungi and Microbes.

https://lab.stajich.org

See our Standard Operating Procedures are (in progress) documentation on procedures and onboarding.

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  1. Phyling Phyling Public

    Phyling: phylogenetic inference from annotated genomes

    Python 30 5

  2. AAFTF AAFTF Public

    Automatic Assembly For The Fungi

    Python 26 6

  3. SOP_data SOP_data Public

    Standard Operating Procedures

    1

  4. funannotate_template funannotate_template Public template

    Project template for doing a funannotate annotation set

    Shell 2 1

  5. PopGenomics_template PopGenomics_template Public template

    Template for Population Genomics variant calling

    Shell 3 2

  6. Comparative_pipeline Comparative_pipeline Public

    Comparative genomics pipeline

    Perl 11 6

Repositories

Showing 10 of 218 repositories
  • Phyling Public

    Phyling: phylogenetic inference from annotated genomes

    stajichlab/Phyling’s past year of commit activity
    Python 30 MIT 5 3 0 Updated Jan 30, 2026
  • stajichlab.github.io Public Forked from greenelab/lab-website-template

    Stajich Lab Website

    stajichlab/stajichlab.github.io’s past year of commit activity
    HTML 0 BSD-3-Clause 427 0 0 Updated Jan 29, 2026
  • orthoSynAssign Public

    Assign orthologs within many-many groups with synteny

    stajichlab/orthoSynAssign’s past year of commit activity
    Python 0 0 0 0 Updated Jan 23, 2026
  • DhingraLab_Afum_AzoleAdapted Public

    Azole Adapted Afumigatus strain resequencing

    stajichlab/DhingraLab_Afum_AzoleAdapted’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Jan 23, 2026
  • Massospora_RNAseq Public

    Some exploring expression from cicada plugs (2024 samples)

    stajichlab/Massospora_RNAseq’s past year of commit activity
    HTML 0 0 0 0 Updated Jan 22, 2026
  • KassonLab_Mycangium_RNAseq Public

    Mycangium RNAseq

    stajichlab/KassonLab_Mycangium_RNAseq’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Jan 15, 2026
  • PopGenomics_template Public template

    Template for Population Genomics variant calling

    stajichlab/PopGenomics_template’s past year of commit activity
    Shell 3 MIT 2 2 0 Updated Jan 7, 2026
  • PopGenomics_Coccidioides_2025 Public

    Combined analysis set for 2025 freeze of Coccidioides strains

    stajichlab/PopGenomics_Coccidioides_2025’s past year of commit activity
    Shell 0 0 0 0 Updated Dec 19, 2025
  • CramerLab_Afumigatus_AF293_VOR Public Forked from stajichlab/PopGenomics_Afumigatus_CEA10

    Explore AF293 VOR Strain Evolution

    stajichlab/CramerLab_Afumigatus_AF293_VOR’s past year of commit activity
    HTML 0 MIT 1 0 0 Updated Dec 18, 2025
  • DhingraLab_ncRNA_Afumigatus Public

    Afumigatus ncRNA discovery from RNASeq and comparative approach

    stajichlab/DhingraLab_ncRNA_Afumigatus’s past year of commit activity
    R 0 MIT 0 0 0 Updated Nov 21, 2025
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