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Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,578 skills3 installs3,530 views
- Biomedical Rag Citation Pipelines--> --- name: bio-biomedical-rag-citation-pipelines description: Design citation-grounded biomedical retrieval and generation systems for literature-heavy assistants. Use when building or improving PubMed or PMC search pipelines, hybrid retrieval, claim-to-citation validation, evidence-aware answer synthesis, or evaluation workflows for biomedical RAG applications. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minute...Votes: 0GitHub stars: 32
- Ngs Analysis--> --- name: bio-ngs-analysis description: Practical next-generation sequencing analysis support for bulk RNA-seq, variant calling, alignment, preprocessing, and workflow assembly. Use when working from FASTQ or BAM/VCF inputs, setting up QC, choosing aligners or quantifiers, organizing reproducible NGS pipelines, or preparing downstream differential or variant analyses. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15...Votes: 0GitHub stars: 32
- Skill Library Maintainer--> --- name: bio-skill-library-maintainer description: Maintain and improve large skill repositories with consistent metadata, lean SKILL.md bodies, reusable references, and validation discipline. Use when auditing skill collections, normalizing frontmatter, splitting oversized skills into references, adding new skills, updating agents/openai.yaml, or preparing a curated skills repo for release. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully wi...Votes: 0GitHub stars: 32
- Technical Writing--> --- name: technical-writing-expert description: Create comprehensive, clear, and structured technical documentation, reports, and whitepapers. keywords: - documentation - reporting - markdown - latex - clarity - structure measurable_outcome: Produce a 2000-word technical report with <1% grammatical errors and >90% clarity score (Flesch-Kincaid) within 1 hour. license: MIT metadata: author: AI Agentic Skills Team version: "2.0.0" compatibility: - system: any allowed-tools: - read_file - wr...Votes: 0GitHub stars: 32
- Bulkrna Batch CorrectionBatch effect correction for multi-cohort bulk RNA-seq data using ComBat, with PCA-based visualization before and after correction.Votes: 0GitHub stars: 32
- Bulkrna CoexpressionWGCNA-style weighted gene co-expression network analysis — module detection, soft thresholding, hub genes.Votes: 0GitHub stars: 32
- Bulkrna DeDifferential expression analysis via PyDESeq2 with Welch's t-test fallback — volcano plots, MA plots, p-value diagnostics.Votes: 0GitHub stars: 32
- Bulkrna DeconvolutionBulk RNA-seq cell type deconvolution using NNLS (built-in), with optional CIBERSORTx and MuSiC bridges.Votes: 0GitHub stars: 32
- Bulkrna EnrichmentPathway enrichment analysis for bulk RNA-seq — ORA and GSEA via GSEApy, with built-in hypergeometric fallback.Votes: 0GitHub stars: 32
- Bulkrna Geneid MappingGene identifier conversion between Ensembl, Entrez, HGNC symbols, and UniProt for bulk RNA-seq count matrices.Votes: 0GitHub stars: 32
- Bulkrna Ppi NetworkProtein-protein interaction network analysis from DEG lists — STRING API query, graph construction, hub gene identification.Votes: 0GitHub stars: 32
- Bulkrna QcBulk RNA-seq count matrix quality control — library sizes, gene detection, sample correlation, outlier detection, CPM normalization.Votes: 0GitHub stars: 32
- Bulkrna Read AlignmentRNA-seq read alignment and quantification statistics — STAR/HISAT2/Salmon log parsing, mapping rate, unique/multi-mapped reads, library strandedness, gene body coverage.Votes: 0GitHub stars: 32
- Bulkrna Read QcFASTQ quality assessment for bulk RNA-seq — Phred scores, GC content, adapter detection, read length distribution, Q20/Q30 rates.Votes: 0GitHub stars: 32
- Bulkrna SplicingAlternative splicing analysis — PSI quantification, differential splicing event detection from rMATS/SUPPA2 output.Votes: 0GitHub stars: 32
- Bulkrna SurvivalSurvival analysis for bulk RNA-seq — Kaplan-Meier curves, Cox proportional hazards, expression-based patient stratification.Votes: 0GitHub stars: 32
- Bulkrna TrajblendBulk-to-single-cell trajectory interpolation — uses VAE and GNN to bridge bulk RNA-seq with single-cell reference data, generating synthetic single-cell profiles and embedding bulk samples into developmental trajectories.Votes: 0GitHub stars: 32
- Genomics AlignmentAlignment statistics from SAM/BAM files: mapping rate, MAPQ distribution, insert size, duplicate rate, proper pair rate. Mirrors samtools-flagstat.Votes: 0GitHub stars: 32
- Genomics AssemblyGenome assembly quality assessment: N50/N90/L50/L90 (QUAST-compatible), GC content, contig length distribution, completeness estimation. Wraps SPAdes, Megahit, Flye, Canu.Votes: 0GitHub stars: 32
- Genomics Cnv CallingCopy number variant detection from exome/WGS data using CNVkit, Control-FREEC, or GATK gCNV. Supports tumor-normal pairs, tumor-only, and germline modes.Votes: 0GitHub stars: 32
- Genomics EpigenomicsEpigenomics analysis including ATAC-seq peak calling with MACS3, ChIP-seq analysis, motif enrichment, and chromatin accessibility.Votes: 0GitHub stars: 32
- Genomics PhasingHaplotype phasing analysis: phase block N50, phased fraction, PS (Phase Set) field parsing, pipe-delimited genotype detection. Wraps WhatsHap, SHAPEIT5, Eagle2.Votes: 0GitHub stars: 32
- Genomics QcFASTQ quality control: Phred quality scores, GC/N content, Q20/Q30 rates, per-base quality profiles, read length distribution, and adapter contamination detection.Votes: 0GitHub stars: 32
- Genomics Sv DetectionStructural variant detection (DEL/DUP/INV/TRA): SV VCF parsing with BND notation, size classification (50bp-10Mb), evidence types. Wraps Manta, Lumpy, Delly, Sniffles.Votes: 0GitHub stars: 32
- Genomics Variant AnnotationVariant functional impact prediction: VEP consequence types (HIGH/MODERATE/LOW/MODIFIER), SIFT, PolyPhen-2, and CADD scoring. Rule-based annotation engine for demo, wraps VEP/snpEff/ANNOVAR.Votes: 0GitHub stars: 32
- Genomics Variant CallingGermline and somatic variant calling (SNVs, Indels) using GATK HaplotypeCaller, Mutect2, DeepVariant, or FreeBayes. Includes GVCF workflow, VQSR, and hard filtering.Votes: 0GitHub stars: 32
- Genomics Vcf OperationsVCF operations: multi-allelic parsing, variant classification (SNP/MNP/INS/DEL/COMPLEX), Ti/Tv ratio, QUAL/DP filtering, INFO field parsing. Mirrors bcftools stats.Votes: 0GitHub stars: 32
- LiteratureParse scientific literature (PDFs, URLs, DOIs) to extract GEO accessions, metadata, and datasets. Use when users provide a paper and want to automatically extract data sources for downstream omics analysis.Votes: 0GitHub stars: 32
- Metabolomics AnnotationMetabolite annotation and structural identification using SIRIUS, CSI:FingerID, GNPS, or MetFrag.Votes: 0GitHub stars: 32
- Metabolomics DeMetabolomics differential analysis using univariate tests (t-test, FDR), multivariate methods (PCA, PLS-DA, OPLS-DA, sPLS-DA), Random Forest, and ROC analysis for biomarker discovery.Votes: 0GitHub stars: 32
- Metabolomics NormalizationMetabolomics data normalization, scaling and transformation.Votes: 0GitHub stars: 32
- Metabolomics Pathway EnrichmentMetabolomics pathway analysis using MetaboAnalystR (KEGG, Reactome), pathview visualization, MSEA, mummichog, and network-based topology analysis.Votes: 0GitHub stars: 32
- Metabolomics Peak DetectionPeak picking, feature detection, alignment and grouping using XCMS, MZmine 3, or MS-DIAL.Votes: 0GitHub stars: 32
- Metabolomics QuantificationFeature quantification, missing value imputation, and normalization for metabolomics data.Votes: 0GitHub stars: 32
- Metabolomics StatisticsStatistical analysis for metabolomics — PCA, PLS-DA, clustering, and univariate tests.Votes: 0GitHub stars: 32
- Metabolomics Xcms PreprocessingXCMS3 workflow for LC-MS/GC-MS metabolomics preprocessing. Peak detection (CentWave/MatchedFilter), RT alignment (Obiwarp), correspondence, gap filling, and CAMERA adduct/isotope annotation.Votes: 0GitHub stars: 32
- OrchestratorMulti-omics query routing and pipeline orchestration across all OmicsClaw domains. Routes natural language queries to the correct analysis skill across spatial transcriptomics, single-cell omics, genomics, proteomics, and metabolomics.Votes: 0GitHub stars: 32
- Omics Skill BuilderCreate OmicsClaw-native skill scaffolds for new reusable workflows that are not yet represented in the current skill catalog.Votes: 0GitHub stars: 32
- Proteomics Data ImportImport and convert proteomics data formats between MaxQuant, DIA-NN, Spectronaut, and standard CSV.Votes: 0GitHub stars: 32
- Proteomics DeDifferential protein abundance testing using MSstats, limma, proDA, and scipy/statsmodels for Python. Multiple testing correction with BH FDR.Votes: 0GitHub stars: 32
- Proteomics EnrichmentPathway, network, and functional enrichment for proteomics using STRING, DAVID, or g:Profiler.Votes: 0GitHub stars: 32
- Proteomics IdentificationDatabase search for peptide/protein identification using MaxQuant, MS-GF+, Comet, or Mascot.Votes: 0GitHub stars: 32
- Proteomics Ms QcMass spectrometry raw data quality control using PTXQC, rawTools, or MSstatsQC.Votes: 0GitHub stars: 32
- Proteomics PtmPost-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Site localization, motif analysis, and quantitative PTM analysis with MSstatsPTM.Votes: 0GitHub stars: 32
- Proteomics QuantificationProtein/peptide quantification (LFQ, TMT, DIA) using MaxQuant LFQ, DIA-NN, or Skyline.Votes: 0GitHub stars: 32
- Proteomics StructuralStructural proteomics and cross-linking MS analysis using XlinkX, pLink, or xiSEARCH.Votes: 0GitHub stars: 32
- Scatac PreprocessingSingle-cell ATAC-seq preprocessing with a Signac-style TF-IDF + LSI workflow. Performs cell and peak filtering, top-peak selection, TF-IDF normalization, latent semantic indexing, neighborhood graph construction, UMAP, and Leiden clustering, then exports a downstream-ready AnnData plus a standard OmicsClaw gallery and reproducibility bundle.Votes: 0GitHub stars: 32
- Sc Ambient RemovalRemove ambient RNA contamination from droplet-based single-cell RNA-seq using a simple subtraction path, CellBender, or SoupX. The wrapper exposes only the parameters that are actually wired into the current implementation.Votes: 0GitHub stars: 32
- Sc Batch IntegrationIntegrate multi-sample scRNA-seq data with Harmony, scVI, scANVI, BBKNN, Scanorama, or supported R-backed integration methods.Votes: 0GitHub stars: 32
- Sc Cell AnnotationAnnotate cell types from normalized scRNA-seq data using marker scoring, CellTypist, PopV-style reference mapping, lightweight KNNPredict-style mapping, SingleR, or scmap through shared Python/R backends.Votes: 0GitHub stars: 32