Paul Pavlidis
Community@ppavlidis · Vancouver, BC
Paul Pavlidis's skill registry delivers reproducible bioinformatics, genomics analysis, provenance tracking, and publication-grade scientific figure and manuscript tooling.
Agent Skills by Paul Pavlidis
Showing 15 vetted skills indexed across 1 GitHub repositories.
ppavlidissupplementary-table
Write supplementary tables in xlsx, csv, and tsv with embedded figure provenance metadata.
ppavlidispdf-extract
Extract text, metadata, and annotations from PDF files with provenance sidecars.
ppavlidisprovenance-stamp
Write and verify sha256 provenance sidecars for analysis artifacts.
ppavlidisontology-terms
Query parents, children, definitions, and search results for OBO biomedical ontology terms.
ppavlidisarchitecture-figures
Generate publication-grade architecture, pipeline, lifecycle, and Gantt figures with matplotlib primitives.
ppavlidisnextflow-authoring
Write, structure, and debug Nextflow DSL2 workflows and modules following nf-core conventions.
ppavlidiszotero-plugin
Build, debug, and release Zotero 7-9 plugins using classic bootstrap or TypeScript toolkit stacks.
ppavlidisgene-statistics
Computes per-gene multifunctionality scores from GO annotations to flag habitual top-hit genes.
ppavlidisgget
Query 20+ bioinformatics databases for genes, sequences, structures, and expression data.
ppavlidismethods-section
Extracts tool versions and provenance from lockfiles to draft academic Methods sections.
ppavlidisgene-set-fetch
Fetches provenance-stamped gene sets from Ensembl, Lambert 2018, JASPAR, and disease databases into TSV files.
ppavlidisplotting
Generate publication-grade heatmaps, scatter plots, stripcharts, boxplots, and density plots in R and Python.
ppavlidiscitation-validator
Validate bibliography citations against CrossRef, OpenAlex, and PubMed to detect hallucinated references.
ppavlidisenrichment
Runs PR-AUC and hypergeometric gene-set enrichment with multifunctionality correction against GO and GMT libraries.
ppavlidisgene-annotations
Query bidirectional gene-to-GO-term annotations from GOA and GAF sources with provenance.
Frequently Asked Questions About Paul Pavlidis
FAQPage SchemaWhat tasks can I accomplish with Paul Pavlidis's skills?▼
You can run gene-set enrichment with PR-AUC statistics, query GO/MONDO/HP ontology hierarchies, fetch transcription-factor and disease-gene sets, extract PDF text and annotations, stamp sha256 provenance sidecars, validate citations against CrossRef, draft Methods sections, and build publication-grade heatmaps and architecture figures.
Who are these skills designed for?▼
Computational biologists, genomics researchers, and academic scientists who need reproducible analysis artifacts. The skills target users doing enrichment analysis, ontology lookups, manuscript preparation, and figure authoring, plus developers writing Nextflow DSL2 pipelines or Zotero 7-9 plugins.
How do the provenance and reproducibility features work?▼
The provenance-stamp skill writes *_meta.json sidecars recording artifact sha256, input hashes, source URLs, DOIs, and timestamps, importable as a library or run as a CLI. Supplementary-table, pdf-extract, gene-set-fetch, and gene-annotations all emit compatible sidecars for later audit.
Are these skills free and open source?▼
Yes. The gget skill is explicitly distributed under the BSD-2-Clause license, permitting free use and modification. Other skills in the manifest carry no stated license restrictions and are published publicly in the registry alongside 27 public repositories.
What dependencies and data sources do the skills require?▼
PDF extraction uses pymupdf with pypdf fallback; ontology and annotation queries hit OLS at EBI, QuickGO, NCBI gene2go, and Open Targets; enrichment consumes GMT files and GO BP libraries; Methods drafting reads lockfiles like requirements.txt, renv.lock, and conda environment.yaml.