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pegRNA pipeline

Author, private repo

Automated pegRNA design for prime-editing C-terminal protein tagging.

  • PRIDICT 2.0
  • Python
  • Imperial CX3 HPC

This pipeline designs pegRNAs for prime-editing C-terminal protein tagging. It supports the lab's work on tagging proteins in human cells, and it runs on the Imperial CX3 HPC cluster.

It has three design modes, and the person running it picks one to suit the insert. PE7 handles inserts up to 40 bp, TJ-PE handles inserts up to about 500 bp, and PA handles anything larger, including inserts over 1 kb. It uses PRIDICT 2.0 to predict prime-editing efficiency.

The repository is private.

Activity

226 contributions in the last year

Select a day to see what happened.

Monthly totals
MonthCommitsPostsMilestones
November 2025000
December 2025000
January 2026000
February 2026000
March 2026000
April 20266600
May 2026000
June 20264700
July 20269000
August 2026000
September 2026000
October 2026000
November 20262300

Activity updated 3 November 2026

Timeline

November 2026

  • CommitpegRNA-pipeline feat(prod): tunnel failover so a rate-limited provider cannot take the site down
  • CommitpegRNA-pipeline fix(offtarget): mixed-length protospacers aborted the entire cas-offinder run
  • CommitpegRNA-pipeline feat(docking): calibrate from 122 measurements, derive the table from committed data, flag borderline verdicts
  • CommitpegRNA-pipeline fix: a failed design must still disclose which gates were real
  • CommitpegRNA-pipeline feat(prod): tunnel resilience, backend-down UX, operational runbook
  • CommitpegRNA-pipeline fix(guides): one definition of a usable spacer; an explicit, disclosed ngRNA off-target tolerance
  • CommitpegRNA-pipeline feat(ops): named Cloudflare tunnel setup, ready to run once the token exists (#26)
  • CommitpegRNA-pipeline feat(ops): stop a design taking the shared host; cache off-target results
  • CommitpegRNA-pipeline fix(demo): make the real-models demo produce a design; calibrate the docking and folding gates
  • CommitpegRNA-pipeline fix(docking): bound every Boltz-2 call in time; record how the endpoint really waits
  • CommitpegRNA-pipeline test(e2e): scripts/qa-browser.mjs — Playwright check of the live site
  • CommitpegRNA-pipeline feat(ops): scripts/audit-production.sh — one command to prove the deployment
  • CommitpegRNA-pipeline fix(web): stop Vercel builds overwriting the committed frontend; make the demo an acceptance test
  • CommitpegRNA-pipeline feat(prod): zero stand-in gates, long-run streaming, api-mode token
  • CommitpegRNA-pipeline feat(pridict): make the local auto-spacer path actually runnable
  • CommitpegRNA-pipeline feat(deploy): make a no-stand-in production deployment reachable
  • CommitpegRNA-pipeline feat(web): host the UI on Vercel against a remote pipeline backend
  • CommitpegRNA-pipeline docs(deploy): fix the clone step — the repo is private
  • CommitpegRNA-pipeline feat(deploy): PEGRNA_SKIP_PULL — deploy without credentials on the host
  • CommitpegRNA-pipeline Merge pull request #22 from thepigdestroyer/fix/portable-api-mode
  • CommitpegRNA-pipeline fix(deploy): dedupe maxentpy install, support pip-less venvs, cap PRIDICT cores
  • CommitpegRNA-pipeline feat(web): rebuild the frontend as React + TypeScript + Tailwind
  • CommitpegRNA-pipeline fix: make api mode portable + disclose stand-in gates + offline fake mode

July 2026

  • CommitpegRNA-pipeline Merge pull request #15 from neurogenomics/fix/declare-requests-dep
  • CommitpegRNA-pipeline Merge pull request #13 from neurogenomics/feat/stage-f-insert-lever
  • CommitpegRNA-pipeline Merge pull request #14 from neurogenomics/feat/stage-g-parallel-het
  • CommitpegRNA-pipeline fix(web): correct het_snps input schema, refresh het/example flow, add flank guard
  • CommitpegRNA-pipeline Merge pull request #10 from neurogenomics/fix/annotate-docking-floor
  • CommitpegRNA-pipeline docs(docking): annotate the scaffold-Cas9 interface ipTM floor with its AF-multimer band
  • CommitpegRNA-pipeline fix(importance): map insertion footprint to absolute protein residues (ADR 0019)
  • CommitpegRNA-pipeline Merge pull request #7 from neurogenomics/fix/pridict-insert-40bp
  • CommitpegRNA-pipeline feat(cli,web): route design-recoded to het-edit dual pass (Stage 3c)
  • CommitpegRNA-pipeline feat(pridict): PRIDICT-designed ngRNA, pipeline-owned nick selection (Stage 2b)
  • CommitpegRNA-pipeline refactor(tjpe): one canonical design workflow; deprecate legacy orchestrator (Stage H, ADR 0021)
  • CommitpegRNA-pipeline Merge pull request #8 from neurogenomics/fix/importance-mapping-legacy-layout
  • CommitpegRNA-pipeline fix(pridict): truncate cargo to 40bp for auto-spacer editseq (PRIDICT ceiling)
  • CommitpegRNA-pipeline feat(recoded): run reverse-targeting + het-specific designs in parallel (Stage G, ADR 0023)
  • CommitpegRNA-pipeline Merge pull request #6 from neurogenomics/feat/pridict2-wiring
  • CommitpegRNA-pipeline feat(examples): FLAG-tag CTCF auto-spacer config that reaches Boltz-2 docking
  • CommitpegRNA-pipeline fix(deps): declare requests (genome_ingest GRCh38 context fetch)

Showing the latest 40 of 226 events.

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