jaechang-hits/SciAgent-Skills

Tool or topic name samtools (via pysam Python bindings) Category genomics-bioinformatics Skill type toolkit Use case BAM/SAM/CRAM file manipulation: reading alignments, filtering by region/quality/flag, computing coverage/depth, extracting read groups, and indexing. Foundation skill for any NGS analysis pipeline. Official documentation URL https://pysam.readthedocs.io/en/latest/ Why this is a good first issue Toolkit type with well-defined modules (AlignmentFile, TabixFile, VariantFile) Existing pysam skill may need expansion or a dedicated samtools-focused version Very high demand across all NGS workflows

Tool or topic name Open Babel (openbabel / pybel) Category structural-biology-drug-discovery Skill type toolkit Use case Chemical file format conversion and molecular manipulation: convert between SMILES, SDF, MOL2, PDB formats; add hydrogens; generate 3D coordinates; compute simple descriptors. Essential companion to RDKit and AutoDock Vina workflows. Official documentation URL https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python.html Why this is a good first issue Toolkit type with clear independent modules Existing rdkit-cheminformatics and autodock-vina-docking skills for reference Straightforward API with good documentation

Tool or topic name Salmon Category genomics-bioinformatics Skill type pipeline Use case Fast transcript-level quantification from RNA-seq reads: index building, quasi-mapping, quantification, and import into Python (via tximeta/pyroe). Commonly used upstream of DESeq2/PyDESeq2. Official documentation URL https://salmon.readthedocs.io/en/latest/ Why this is a good first issue Clear linear pipeline (index → quant → import) Pairs naturally with existing pydeseq2-differential-expression skill Well-documented with straightforward CLI interface

Tool or topic name Seurat (R/satijalab) Category genomics-bioinformatics Skill type guide Use case Guide for researchers who use Seurat in R and want to understand how to translate their workflows to Python equivalents (Scanpy). Covers: key concept mapping (Seurat object vs AnnData), common workflow differences, and when to use R vs Python. Official documentation URL https://satijalab.org/seurat/ Why this is a good first issue Guide type (prose-centric) — no runnable code required Can reference existing scanpy-scrna-seq skill for Python side High demand from R users transitioning to Python

Tool or topic name CellRanger (10X Genomics) Category genomics-bioinformatics Skill type pipeline Use case Preprocessing 10X Chromium scRNA-seq data: FASTQ generation (cellranger mkfastq), read alignment and gene counting (cellranger count), sample aggregation (cellranger aggr). This is the standard upstream step before Scanpy/Seurat analysis. Official documentation URL https://www.10xgenomics.com/support/software/cell-ranger/latest Why this is a good first issue Well-documented tool with clear linear workflow Existing scanpy-scrna-seq skill can serve as a reference for structure High demand — most scRNA-seq analyses start with CellRanger