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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 31 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 219 repositories
  • AAFTF Public

    Automatic Assembly For The Fungi

    stajichlab/AAFTF’s past year of commit activity
    Python 26 MIT 6 17 0 Updated Mar 3, 2026
  • Phyling Public

    Phyling: phylogenetic inference from annotated genomes

    stajichlab/Phyling’s past year of commit activity
    Python 31 MIT 5 3 1 Updated Mar 3, 2026
  • Fungi_5k Public

    Fungi5k dataset analysis

    stajichlab/Fungi_5k’s past year of commit activity
    Python 1 1 0 0 Updated Feb 28, 2026
  • orthoSynAssign Public

    Assign orthologs within many-many groups with synteny

    stajichlab/orthoSynAssign’s past year of commit activity
    Python 1 GPL-3.0 0 1 0 Updated Feb 24, 2026
  • DhingraLab_Afum_ncRNA_temperature Public

    A. fumigatus Temp and delta-ncRNA analysis

    stajichlab/DhingraLab_Afum_ncRNA_temperature’s past year of commit activity
    R 0 0 0 0 Updated Feb 17, 2026
  • adhesionPred Public

    Adhesion protein prediction

    stajichlab/adhesionPred’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 16, 2026
  • Afumigatus_RefStrains Public

    Reference A. fumigatus strain panel

    stajichlab/Afumigatus_RefStrains’s past year of commit activity
    Shell 1 0 0 0 Updated Feb 13, 2026
  • Antarctica_Endolithic_Eukaryotic_MAG Public

    Eukaryotic MAGs from Endolithic metagenome sampling

    stajichlab/Antarctica_Endolithic_Eukaryotic_MAG’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Feb 12, 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 1 1 0 0 Updated Feb 6, 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 431 0 0 Updated Jan 29, 2026
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Most used topics

bioinformatics fungi