Skill UI

deepTools is a Python command-line suite for NGS workflows, converting BAM files into normalized coverage, running QC (fingerprint, correlation, PCA), comparing samples, and rendering heatmaps or profiles for ChIP-seq, RNA-seq, and ATAC-seq analyses.

FlowIO reads and writes Flow Cytometry Standard (FCS) files, exposing metadata, channels, and NumPy event arrays while allowing CSV/DataFrame conversion, making it ideal for cytometry pipelines and backend preprocessing services.

Connect to NCBI's GEO repository, search series/samples/platforms via Entrez queries, fetch profiles, and download raw/processed matrices using GEOparse for transcriptomics and expression analysis workflows.

GeoPandas extends pandas for geospatial vector data, enabling reading/writing shapefiles, GeoJSON, GeoPackage and PostGIS, performing CRS management, spatial joins, overlays, buffering, area/distance calculations, and producing static or interactive choropleth maps.

Query and download the NCI Imaging Data Commons public cancer imaging datasets via idc-index, filter by metadata, fetch DICOM files, visualize series, and respect licensing details for AI training or research.

LatchBio Integration provides a Python-first platform to compose, deploy, and monitor serverless bioinformatics pipelines with the Latch SDK, decorator-based tasks, cloud storage (LatchFile/Dir), GPU tuning, and Nextflow or Snakemake interoperability.

MarkItDown converts PDFs, DOCX, PPTX, XLSX, HTML, JSON, XML, archives, YouTube links, images via OCR, and audio via transcription into clean Markdown, providing token-efficient text ready for LLMs and documentation workflows.

Modal delivers cloud-native serverless Python with on-demand GPUs, persistent storage, and web endpoints to deploy ML workloads, batch jobs, and APIs without writing Dockerfiles.

Access RCSB PDB to search biomolecular structures via text, sequence, or geometry queries, download coordinate files in PDB/mmCIF/Binary formats, retrieve metadata, and batch-process entries for drug discovery, protein engineering, and structural biology pipelines.

This skill provides complete, programmatic integration with the protocols.io API v3, enabling advanced management of scientific protocols. Use it for the entire protocol lifecycle, including discovery by DOI or keywords, creating new protocols, managing steps and materials, coordinating collaborative development, organizing workspaces, and tracking experiments. It covers authentication, file handling, and discussion management, making it ideal for automated lab workflows and scientific documentation systems.

Pydicom is a Python toolkit for reading, writing, and manipulating DICOM medical imaging files, helping teams extract pixel data, manage metadata, anonymize records, convert to standard formats, and integrate with PACS workflows in healthcare research and radiology applications.

scikit-bio provides a Python-native biological data toolkit for reading/writing FASTA/Newick files, manipulating sequences, building alignments and phylogenies, and calculating diversity metrics for microbiome and ecology workflows.