Skip to content

Navigation Menu

Appearance settings

stajichlab

GitHub Copilot
Write better code with AI

GitHub Spark New
Build and deploy intelligent apps

GitHub Models New
Manage and compare prompts

GitHub Advanced Security
Find and fix vulnerabilities

Actions
Automate any workflow
Codespaces
Instant dev environments

Issues
Plan and track work

Code Review
Manage code changes

Discussions
Collaborate outside of code

Code Search
Find more, search less
Explore

Why GitHub

Documentation

GitHub Skills

Blog
Integrations

GitHub Marketplace

MCP Registry
View all features
By company size

Enterprises

Small and medium teams

Startups

Nonprofits
By use case

App Modernization

DevSecOps

DevOps

CI/CD

View all use cases
By industry

Healthcare

Financial services

Manufacturing

Government

View all industries
View all solutions
Topics

AI

DevOps

Security

Software Development

View all
Explore

Learning Pathways

Events & Webinars

Ebooks & Whitepapers

Customer Stories

Partners

Executive Insights
GitHub Sponsors
Fund open source developers
The ReadME Project
GitHub community articles
Repositories

Topics

Trending

Collections
Enterprise platform
AI-powered developer platform
Available add-ons

GitHub Advanced Security
Enterprise-grade security features

Copilot for business
Enterprise-grade AI features

Premium Support
Enterprise-grade 24/7 support
Pricing

Search code, repositories, users, issues, pull requests...

Search

Clear

Search syntax tips

Provide feedback

We read every piece of feedback, and take your input very seriously.

Include my email address so I can be contacted

Saved searches

Use saved searches to filter your results more quickly

Name

Query

To see all available qualifiers, see our documentation.

Appearance settings

You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session.

Dismiss alert

Jason Stajich Lab at UC Riverside

Evolutionary Genomics of Fungi projects, data and software

33 followers
RIverside, CA
http://lab.stajich.org
@stajichlab
jason.stajich@ucr.edu

Overview
Repositories
Projects
Packages
People

More

Overview
Repositories
Projects
Packages
People

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.

Pinned Loading

Phyling Phyling Public

Phyling: phylogenetic inference from annotated genomes

Python 27 5
AAFTF AAFTF Public

Automatic Assembly For The Fungi

Python 25 5
SOP_data SOP_data Public

Standard Operating Procedures

1
funannotate_template funannotate_template Public template

Project template for doing a funannotate annotation set

Shell 2 1
PopGenomics_template PopGenomics_template Public template

Template for Population Genomics variant calling

Shell 3 2
Comparative_pipeline Comparative_pipeline Public

Comparative genomics pipeline

Perl 11 6

Repositories

Loading

Type

Select type

All Public Sources Forks Archived Mirrors Templates

Language

Select language

All Go HTML JavaScript Jupyter Notebook Nextflow Pep8 Perl Python R Roff Scala Scheme Shell TeX

Sort

Select order

Last updated Name Stars

Showing 10 of 215 repositories

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 418 0 0 Updated Nov 14, 2025
Acarospora_socialis_pangenome Public
Pangenome from A. socialis CCGP and herbarium resequencing project

stajichlab/Acarospora_socialis_pangenome’s past year of commit activity

Shell 0 0 0 0 Updated Nov 12, 2025
Phyling Public
Phyling: phylogenetic inference from annotated genomes

stajichlab/Phyling’s past year of commit activity

Python 27 MIT 5 3 2 Updated Oct 27, 2025
Fungi_5k Public
Fungi5k dataset analysis

stajichlab/Fungi_5k’s past year of commit activity

Python 0 1 0 0 Updated Oct 27, 2025
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 Oct 25, 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 Sep 29, 2025
AAFTF Public
Automatic Assembly For The Fungi

stajichlab/AAFTF’s past year of commit activity

Python 25 MIT 5 17 0 Updated Sep 15, 2025
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 Sep 3, 2025
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 Aug 22, 2025
ExtremeRhodotorula_RefGenomes Public
Reference Genome Assembly and Annotation for Rhodotorula genomes in "Extreme Rhodotorula" project

stajichlab/ExtremeRhodotorula_RefGenomes’s past year of commit activity

Shell 0 MIT 0 0 0 Updated Jul 2, 2025

View all repositories

People

Top languages

Loading…

Uh oh!

There was an error while loading. Please reload this page.

Most used topics

Loading…

Uh oh!

There was an error while loading. Please reload this page.

Footer

© 2025 GitHub, Inc.

Footer navigation

Terms
Privacy
Security
Status
Community
Docs
Contact

You can’t perform that action at this time.