Agent Skills by Danilo Monge
Showing 42 vetted skills indexed across 1 GitHub repositories.
danilomongedemo
Run the nf-core demo pipeline with validated parameters and pinned release metadata.
danilomongemag
Run the nf-core/mag metagenomics pipeline from samplesheet to annotated outputs.
danilomongesarek
Plan and configure nf-core/sarek variant analysis runs from samplesheets.
danilomongemagmap
Run the nf-core/magmap pipeline for validated read mapping against large genome collections.
danilomongefastquorum
Run the nf-core/fastquorum consensus-read pipeline from a validated samplesheet.
danilomongemarsseq
Run the pinned nf-core marsseq preprocessing pipeline from a validated samplesheet.
danilomongehgtseq
Run the nf-core hgtseq pipeline from a samplesheet with validated parameters.
danilomongemetaboigniter
Orchestrate nf-core/metaboigniter runs for mass spectrometry metabolomics data processing.
danilomongedenovotranscript
Provides automated NLP-based extraction of data from clinical documents and reports.
danilomongecircdna
Run the nf-core/circdna pipeline to identify circular DNA from sequencing data.
danilomongedetaxizer
Run nf-core/detaxizer to identify and remove target taxa from genomic FASTQ data.
danilomongecallingcards
Run the nf-core/callingcards pipeline for Calling Cards sequencing data.
danilomongedifferentialabundance
Automate nf-core differential abundance analyses with validated samplesheets and reproducible outputs.
danilomongecutandrun
Run nf-core/cutandrun workflows for CUT&RUN, CUT&Tag, and TIPseq data.
danilomongeairrflow
Runs nf-core/airrflow immune-repertoire analysis from raw reads or assembled data.
danilomongecreatepanelrefs
Generate validated run metadata and parameter guidance for nf-core/createpanelrefs pipelines.
danilomongelongraredisease
Run the nf-core/longraredisease pipeline from a validated samplesheet and reference genome.
danilomongechipseq
Orchestrate nf-core ChIP-seq peak calling and downstream analysis from a CSV samplesheet.
danilomongeampliseq
Run the nf-core/ampliseq pipeline for amplicon sequencing analysis.
danilomongeatacseq
Execute the nf-core/atacseq workflow for ATAC-seq alignment, peak calling, QC, and differential analysis.
danilomongemetapep
Orchestrate nf-core/metapep pipeline runs for reproducible epitope predictions from metagenomic samples.
danilomongebamtofastq
Convert BAM or CRAM inputs into FASTQ outputs for nf-core bamtofastq runs.
danilomongedemultiplex
Generate validated execution plans for nf-core/demultiplex runs.
danilomongedrop
Run the DROP nf-core pipeline to detect aberrant expression, splicing, and mono-allelic expression from RNA sequencing data.