Skill UI

Comprehensive Python toolkit for molecular biology: sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access. Ideal for batch processing, custom bioinformatics pipelines, and BLAST automation.

Unified Python interface to 40+ bioinformatics web services for cross-database queries, identifier mapping, sequence analysis, and pathway discovery in a single workflow.

Pythonic RDKit wrapper for molecular cheminformatics: parse and standardize SMILES, compute descriptors and fingerprints, cluster compounds, generate 3D conformers, and run parallel drug-discovery workflows.

DeepTools is a comprehensive Python command-line toolkit for processing and analyzing high-throughput sequencing data. It supports quality control, normalization, sample comparison, and generating publication-quality visualizations for ChIP-seq, RNA-seq, and ATAC-seq experiments. Key features include converting BAM to bigWig, assessing sequencing depth, creating heatmaps around genomic features, and performing correlation analysis. Ideal for bioinformatics workflows requiring robust genomic data processing and visualization.

Geniml validates genomic interval workflows, BED files, and model compatibility for ML/statistical analysis. Plan Region2Vec/scEmbed runs, inspect tokenizers, and assess consensus universes locally without network requests. Requires Python 3.10+ and uv for reproducible bioinformatics ML pipelines.

Unified CLI and Python interface to 20+ bioinformatics databases for gene info, BLAST/BLAT, viral sequences, AlphaFold structures, enrichment, disease and expression queries.

Build, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Nextflow, Snakemake, Latch Data, Registry, and MCP. Covers resource configuration, data management, UI forms, and run monitoring.

High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Supports overlap, nearest, merge, coverage, complement and subtract for BED/VCF/BAM/GFF files, with streaming and cloud-native access as a faster bioframe alternative.

A Python library for reading, querying, filtering, and writing genomic file formats including SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, and tabix data. Supports pileup, coverage analysis, indexing, and CRAM reference operations with HTSlib integration. Ideal for bioinformatics workflows requiring low-level streaming access to genomic data.

Python cheminformatics toolkit for fine-grained molecular control: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D coordinate generation, similarity, reactions, and visualization.

Python toolkit for biological data: sequence manipulation, pairwise and multiple alignment, phylogenetic trees, alpha/beta diversity and UniFrac metrics, ordination (PCoA), PERMANOVA, and FASTA/Newick/BIOM I/O for microbiome analysis.

This skill automates the nf-core/pacsomatic pipeline for matched tumor-normal variant calling from BAM files. It handles input validation, samplesheet generation, dry-run checks, and submission to schedulers like Slurm or LSF. Ideal for reproducible bioinformatics analysis execution and troubleshooting pipeline failures.