Provides automated NLP-based extraction of data from clinical documents and reports.
npx skills add https://github.com/danilomonge/nf-claw --skill denovotranscript
Please help me install this Agent Skill. Skill: denovotranscript Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/denovotranscript Command: npx skills add https://github.com/danilomonge/nf-claw --skill denovotranscript
This Skill removes the guesswork from running nf-core/denovotranscript by turning a bulk RNA-seq samplesheet into a reproducible de novo transcriptome assembly workflow with clear input, output, and parameter guidance.
Ask the denovotranscript skill to run nf-core/denovotranscript for my samplesheet and output directory using an appropriate execution profile.
High-intent search queries and answers about installing and using this skill.
A de novo transcriptome assembly workflow processes paired-end RNA-seq reads through QC, trimming, assembly, redundancy reduction, pseudoalignment, and quantification. It requires a validated samplesheet, output paths, and schema-checked parameters for consistent execution.
Schema-driven parameter validation surfaces required inputs, allowed values, defaults, and constraints for nf-core workflows. This ensures runs stay consistent and fail fast on invalid settings before processing your RNA-seq data.
Yes, de novo transcriptome assembly processes paired-end short reads without a reference genome. The workflow performs assembly directly from bulk RNA-seq data, followed by pseudoalignment and quantification for expression analysis.
An end-to-end RNA-seq assembly workflow includes quality control, read trimming, de novo assembly, redundancy reduction, pseudoalignment, and quantification. These steps are validated and executed in one pipeline for reproducible transcriptome results.
The workflow requires validated input and output paths plus schema-checked parameters for deterministic execution. Invalid samplesheet paths or parameters trigger fail-fast behavior to prevent inconsistent transcriptome assembly runs.
danilomongeRun the nf-core/hlatyping workflow on samplesheet-based DNA or RNA sequencing data.
zongtingweiDetect and interpret RNA modification signals from MeRIP-seq sequencing data.
danilomongeGenerate and run nf-core rnaseq workflows from CSV samplesheets.
giadaf-booshaAutomate sequencing data analysis with nf-core bioinformatics pipelines.
