bulk-rnaseq
K-Dense-AI
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCoun…
DesignClaude Code
38.5KGitHub
OPENAGENTSKILL / DIRECTORY
AI Agent Skills
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Results · “rna-seq-quantification”
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Results: 19
Salmon
COMBINE-lab
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Geo ScienceReview before use
893GitHub
PyDESeq2
scverse
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Geo ScienceReview before use
753GitHub
Omicverse
omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Geo ScienceReview before use
1KGitHub
arboreto
K-Dense-AI
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, sin…
DataClaude Code
34KGitHub
Single Cell Pseudotime
agitter
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
Geo ScienceReview before use
444GitHub
alterlab-arboreto
AlterLab-IEU
Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation.…
DesignClaude Code
66GitHub
MLLMCelltype
cafferychen777
Cell type annotation for single-cell RNA-seq using multi-LLM consensus
Geo ScienceReview before use
646GitHub
bio-database-evidence
foryourhealth111-pixel
Unified biological database evidence owner. Use for gene annotation, variant clinical significance, cancer mutation evidence, GWAS trait associations, pathway mapping, t…
DesignClaude Code
3.1KGitHub
SciAgent Skills
jaechang-hits
197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers Omic…
208GitHub
single-cell-annotation
jaechang-hits
Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
AutomationClaude Code
359GitHub
omics-plotting
jaechang-hits
omics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in…
DesignClaude Code
359GitHub
CyteType
NygenAnalytics
Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data
Agent FrameworksReview before use
132GitHub
alterlab-borzoi
AlterLab-IEU
Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP covera…
66GitHub
alterlab-cellxgene
AlterLab-IEU
Query the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnDa…
DesignClaude Code
66GitHub
Sage
lazear
Proteomics search & quantification so fast that it feels like magic
Geo ScienceReview before use
297GitHub
External platform skills
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