Skip to content

Navigation Menu

Appearance settings

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
- EXPLORE BY TOPIC
  AI
  Software Development
  DevOps
  Security
  View all topics
- EXPLORE BY TYPE
  Customer stories
  Events & webinars
  Ebooks & reports
  Business insights
  GitHub Skills
- SUPPORT & SERVICES
  Documentation
  Customer support
  Community forum
  Trust center
  Partners
View all resources
- COMMUNITY
  GitHub SponsorsFund open source developers
- PROGRAMS
  Security Lab
  Maintainer Community
  Accelerator
  GitHub Stars
  Archive Program
- REPOSITORIES
  Topics
  Trending
  Collections
- ENTERPRISE SOLUTIONS
  Enterprise platformAI-powered developer platform
- AVAILABLE ADD-ONS
  GitHub Advanced SecurityEnterprise-grade security features
  Copilot for BusinessEnterprise-grade AI features
  Premium SupportEnterprise-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

Uh oh!

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

HelikarLab / COMO Public

Notifications You must be signed in to change notification settings
Fork 8
Star 11

Code
Issues 24
Pull requests 24
Discussions
Actions
Projects
Security and quality
Insights

Additional navigation options

Code
Issues
Pull requests
Discussions
Actions
Projects
Security and quality
Insights

Remove zFPKM#245

Merged

JoshLoecker merged 28 commits into

developHelikarLab/COMO:developfrom

remove-zfpkmHelikarLab/COMO:remove-zfpkmCopy head branch name to clipboard

Feb 10, 2026

Conversation Commits28 (28)Checks Files changed

Merged

Remove zFPKM#245
JoshLoecker merged 28 commits into
developfrom
remove-zfpkm

Commits

Commits on Feb 9, 2026

fix(fpkm): update imports for zFPKM calculation improvements
JoshLoecker
committed
fix(fpkm): use Salmon quantification instead of STAR quantification
JoshLoecker
committed
chore: ruff formatting
JoshLoecker
committed
chore: fill with integers for faster processing
JoshLoecker
committed
chore: remove unnecessary async function usage
JoshLoecker
committed
fix: remove non existant genes from conversion
JoshLoecker
committed
refactor: use more explicit (albeit longer) code to create gene_info dataframe object
JoshLoecker
committed
chore: import required modules
JoshLoecker
committed
refactor: optional argument for fragment data
JoshLoecker
committed
refactor: improve handling for single cell data
JoshLoecker
committed
chore: generalize data type input
JoshLoecker
committed
chore: ruff formatting
JoshLoecker
committed
chore: simplify FPKM/RPKM calculations; properly compute per-gene FPKM scores
JoshLoecker
committed
refactor: move zfpkm calculation to external package
JoshLoecker
committed
chore: use np.bool for boolean array
JoshLoecker
committed
chore: ruff formatting
JoshLoecker
committed
feat: allow setting negative zFPKM results to 0
JoshLoecker
committed
feat: simplification to use external zfpkm package
JoshLoecker
committed
feat: allow providing the fragment size filepath (from rnaseq preprocessing)
JoshLoecker
committed
chore(ruff): reduce max line length
JoshLoecker
committed
chore(ruff): mark unsorted imports as fixable
JoshLoecker
committed
chore(uv): lock pyproject file
JoshLoecker
committed
chore: remove zfpkm related code as it is now an external package
JoshLoecker
committed
revert: remove local pyproject requirement
JoshLoecker
committed
chore: remove zfpkm testing files
JoshLoecker
committed

Commits on Feb 10, 2026

Merge branch 'develop' into remove-zfpkm
JoshLoecker
authored
chore: force sync lock
JoshLoecker
committed
Purge `fast_bioservices` (#246)
JoshLoecker
authored

Footer

© 2026 GitHub, Inc.

Footer navigation

Terms
Privacy
Security
Status
Community
Docs
Contact

You can’t perform that action at this time.