harmony-batch-correction SKILL.md skillA
harmony-batch-correction from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/harmony-batch-correction@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/single-cell/harmony-batch-correction/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 22,517 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Harmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving biology. Run after PCA, before UMAP. Scales to millions of cells. Python (harmonypy, scanpy) and R (Seurat).
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Harmony Batch Correction ## Overview Harmony is a fast, scalable algorithm for batch integration in single-cell data. It takes a PCA embedding (cells × PCs) as input and returns a corrected embedding from which batch effects have been regressed out via iterative soft-clustering and per-cluster linear regression. The corrected embedding is then used to compute neighbors, UMAP, and downstream clustering — the raw count matrix is never modified. Harmony works for single-cell RNA-seq, ATAC-seq, and other omics modalities where a PCA-like embedding is available. ## When to Use - Integrating scRNA-seq datasets from different samples, donors, sequencing runs, or experimental batches that should contain the same cell types - Removing technical variation (library preparation protocol, 10x chemistry version, sequencing depth, sequencing platform) while preserving biological differences between cell types and conditions - Performing fast, scalable batch correction on datasets with millions of cells where deep generative model training would be prohibitively slow …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/harmony-batch-correction@sha256:d3b1cc2fb1a9d89dThe line at the top of this page pins the label git:20260929.7a7d60f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_rhk5ljxdixojezu7)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 41 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 22,517 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 22,566 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 20,625 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 20,516 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (22517 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_rhk5ljxdixojezu7 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/harmony-batch-correction GET https://markdownregistry.com/api/v1/blob/d3b1cc2fb1a9d89d9fea3b8c92770b14998a40377b0956b5d265ccaf9b027261
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.