salmon-rna-quantification SKILL.md skillA
salmon-rna-quantification 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/salmon-rna-quantification@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/rnaseq/salmon-rna-quantification/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 16,037 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM). Builds a k-mer index from transcriptome FASTA, quantifies in minutes. Outputs TPM/count tables (quant.sf) with optional GC- and sequence-bias correction. Integrates with tximeta/tximport for DESeq2/edgeR. Use STAR when a genome-aligned BAM is needed.
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
# Salmon — Fast RNA-seq Quantification ## Overview Salmon quantifies transcript abundance from RNA-seq reads using quasi-mapping — matching reads to a k-mer index of the transcriptome without full genome alignment. This makes Salmon 20–50× faster than alignment-based tools while producing accurate TPM and estimated count values. Salmon corrects for sequence-specific bias (`--seqBias`), GC-content bias (`--gcBias`), and fragment length distribution automatically. Output `quant.sf` files integrate directly with `tximeta` (R) or `pydeseq2` (Python) for differential expression analysis. For improved accuracy, decoy-aware indexing uses the full genome to identify spurious quasi-mappings. ## When to Use - Performing fast RNA-seq quantification when you do not need a genome-aligned BAM file - Running large-scale RNA-seq studies where alignment speed is a bottleneck (Salmon is 20-50× faster than STAR + featureCounts) - Computing TPM and estimated counts from bulk RNA-seq for differential expression with DESeq2 or edgeR - Correcting for GC bias, fragment length, and sequence context bias with `--gcBias --seqBias` …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/salmon-rna-quantification@sha256:b9d54a249f0473c9The 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_5ntxw227jn2kxryz)
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Versions
The registry has recorded 3 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 62 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 16,037 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 16,086 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 14,109 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 (16037 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_5ntxw227jn2kxryz GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/salmon-rna-quantification GET https://markdownregistry.com/api/v1/blob/b9d54a249f0473c93dbb53010cc54b7b021861b9e10f355ae1de1695b02fbfbb
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