All authors
Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,581 skills3 installs3,534 views
- Counts IngestLoad gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X. Use when importing quantification results for downstream analysis.Votes: 0GitHub stars: 32
- Gene Id MappingConvert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources.Votes: 0GitHub stars: 32
- Metadata JoinsMerge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.Votes: 0GitHub stars: 32
- Sparse HandlingWork with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.Votes: 0GitHub stars: 32
- Riboseq PreprocessingPreprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.Votes: 0GitHub stars: 32
- Ribosome StallingDetect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon-specific translation dynamics.Votes: 0GitHub stars: 32
- Translation EfficiencyCalculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying genes with altered translation independent of transcription.Votes: 0GitHub stars: 32
- Tximport WorkflowImport transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when importing transcript counts into R for DESeq2/edgeR.Votes: 0GitHub stars: 32
- Mirge3 AnalysisFast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miRNAs quickly or analyzing isomiR variants and RNA editing.Votes: 0GitHub stars: 32
- Smrna PreprocessingPreprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs. Use when preparing small RNA-seq reads for downstream quantification or discovery analysis.Votes: 0GitHub stars: 32
- Cwl WorkflowsCreate portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collaborators using different systems, or contributing to community workflow registries.Votes: 0GitHub stars: 32
- Nextflow PipelinesCreate scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building portable pipelines with container support, running workflows on cloud platforms (AWS, Google Cloud), or leveraging nf-core community pipelines.Votes: 0GitHub stars: 32
- Snakemake WorkflowsBuild reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution. Use when creating Python-based workflows, automating multi-step analyses with make-like dependency tracking, or running pipelines on HPC clusters with SLURM.Votes: 0GitHub stars: 32
- Wdl WorkflowsCreate portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines. Use when running GATK best practices pipelines, working with Terra/AnVIL platforms, or building workflows for cloud execution on Google Cloud or AWS.Votes: 0GitHub stars: 32
- Chipseq PipelineEnd-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.Votes: 0GitHub stars: 32
- Crispr Editing PipelineEnd-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies including knockouts, base editing, and HDR knockins. Use when designing complete CRISPR editing experiments for gene knockout, correction, or tagging.Votes: 0GitHub stars: 32
- Expression To PathwaysWorkflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization. Use when taking DE results to pathway enrichment.Votes: 0GitHub stars: 32
- Fastq To VariantsEnd-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller. Use when calling variants from raw sequencing reads.Votes: 0GitHub stars: 32
- Genome Assembly PipelineEnd-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches. Use when assembling genomes from raw reads.Votes: 0GitHub stars: 32
- Imc PipelineEnd-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statistics. Use when analyzing imaging mass cytometry data end-to-end.Votes: 0GitHub stars: 32
- Metabolic Modeling PipelineEnd-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA analysis, and gene essentiality prediction. Use when building metabolic models or predicting metabolic phenotypes from genomic data.Votes: 0GitHub stars: 32
- Metabolomics PipelineEnd-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mapping. Use when processing LC-MS metabolomics data.Votes: 0GitHub stars: 32
- Metagenomics PipelineEnd-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling. Use when profiling metagenomic samples.Votes: 0GitHub stars: 32
- Outbreak PipelineEnd-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen transmission chains.Votes: 0GitHub stars: 32
- Proteomics PipelineEnd-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma. Use when processing mass spectrometry proteomics.Votes: 0GitHub stars: 32
- Riboseq PipelineEnd-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.Votes: 0GitHub stars: 32
- Smrna PipelineEnd-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data.Votes: 0GitHub stars: 32
- Somatic Variant PipelineEnd-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer genomics. Use when calling somatic mutations from tumor-normal pairs.Votes: 0GitHub stars: 32
- Splicing PipelineEnd-to-end alternative splicing analysis from FASTQ to differential splicing results. Aligns with STAR 2-pass mode, performs junction QC, runs rMATS-turbo for differential analysis, and generates sashimi visualizations. Use when performing comprehensive splicing analysis from raw RNA-seq data.Votes: 0GitHub stars: 32
- Tcr PipelineEnd-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.Votes: 0GitHub stars: 32
- Bioinformatics Singlecell--> --- name: bio-bioinformatics-singlecell description: Single-cell and multi-omic analysis for hematology, oncology, and translational biology. Use when working with scRNA-seq, CITE-seq, scATAC-seq, multiome, trajectory analysis, batch correction, cell typing, differential expression, or publication-ready figures in Scanpy, scvi-tools, Seurat, or MuData workflows. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minut...Votes: 0GitHub stars: 32
- Computational Software Development--> --- name: bio-computational-software-development description: Full-stack computational software development for biomedical and life science applications. Use when building or refactoring research software, LLM-enabled analysis platforms, scientific web apps, data pipelines, RAG systems, evaluation harnesses, or package-quality Python services for translational research. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within ...Votes: 0GitHub stars: 32
- Mpn Research Assistant--> --- name: bio-mpn-research-assistant description: Myeloproliferative neoplasm research support across JAK2, CALR, MPL, PPM1D, megakaryocyte biology, fibrosis, clonal evolution, and translational oncology. Use when synthesizing MPN literature, structuring hypotheses, interpreting MPN datasets, summarizing biomarkers, or connecting molecular findings to clinical and experimental follow-up. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with va...Votes: 0GitHub stars: 32
- Python Package Builder--> --- name: python-package-builder description: "Build and publish professional Python packages to PyPI. Use when creating pip-installable packages, converting scripts to packages, setting up pyproject.toml/setup.py, adding CLI interfaces, writing tests, or preparing for PyPI upload. Covers bioinformatics tool packaging." license: Proprietary ---Votes: 0GitHub stars: 32
- Compartment Analysis--> --- name: bio-hi-c-analysis-compartment-analysis description: Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices. Use when identifying A/B compartments from Hi-C data. tool_type: python primary_tool: cooltools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Detect A/B compartment...Votes: 0GitHub stars: 32
- Contact Pairs--> --- name: bio-hi-c-analysis-contact-pairs description: Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs. tool_type: cli primary_tool: pairtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Process Hi-C read pairs with pairtools.Votes: 0GitHub stars: 32
- Hic Data Io--> --- name: bio-hi-c-analysis-hic-data-io description: Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices. tool_type: mixed primary_tool: cooler measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Load and manipulate Hi-C co...Votes: 0GitHub stars: 32
- Hic Differential--> --- name: bio-hi-c-analysis-hic-differential description: Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions. tool_type: python primary_tool: cooltools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Comp...Votes: 0GitHub stars: 32
- Hic Visualization--> --- name: bio-hi-c-analysis-hic-visualization description: Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features. tool_type: python primary_tool: cooltools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Visualize Hi-C c...Votes: 0GitHub stars: 32
- Loop Calling--> --- name: bio-hi-c-analysis-loop-calling description: Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts. Use when detecting chromatin loops from Hi-C data. tool_type: mixed primary_tool: cooltools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Detect chromatin loops an...Votes: 0GitHub stars: 32
- Matrix Operations--> --- name: bio-hi-c-analysis-matrix-operations description: Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices. tool_type: python primary_tool: cooltools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Balance, nor...Votes: 0GitHub stars: 32
- Tad Detection--> --- name: bio-hi-c-analysis-tad-detection description: Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure. Use when calling TADs from Hi-C insulation scores. tool_type: mixed primary_tool: cooltools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Call topologically asso...Votes: 0GitHub stars: 32
- AI Provider GitHub Maintainers 2026--> --- name: ai-provider-github-maintainers-2026 description: Track official AI provider GitHub repositories and release health for reliable integrations. Use when auditing SDK freshness, selecting maintained repos, or planning upgrades based on release cadence and issue velocity. measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- AWS Bedrock Operations 2026Build and run production workloads on Amazon Bedrock with current model availability, Converse API, agents, guardrails, AgentCore, and IAM controls. Use when implementing Bedrock inference pipelines, managed agents, or provider-agnostic model routing on AWS.Votes: 0GitHub stars: 32
- Anthropic Claude Operations 2026--> --- name: anthropic-claude-operations-2026 description: Integrate and operate Anthropic Claude APIs with current model lifecycle guidance. Use when implementing Claude-based assistants, tool use, long-context reasoning, or when planning model upgrades based on release notes and deprecations. measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Azure AI Foundry Operations 2026Implement and operate Azure AI Foundry and Microsoft Foundry workloads with explicit identity, deployment, model versioning, safety, and agent-service controls. Use when deploying model endpoints, migrating model versions, or setting up production guardrails on Azure.Votes: 0GitHub stars: 32
- Cloud AI Operations AWS Azure 2026--> --- name: cloud-ai-operations-aws-azure-2026 description: Operate AI workloads on AWS Bedrock and Azure AI/Azure OpenAI with production-focused cloud controls. Use when selecting managed model providers, implementing enterprise auth, and designing resilient cloud-native inference pipelines. measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Cohere Platform Operations 2026Integrate and operate Cohere APIs with current model, rerank, embedding, transcribe, and SDK guidance. Use when selecting Cohere models, building search or agent workflows, or planning migration across Cohere platform updates.Votes: 0GitHub stars: 32
- DeepSeek API Operations 2026Integrate and operate DeepSeek APIs with current docs and compatibility guidance. Use when implementing DeepSeek chat, reasoning, tool calling, or FIM workflows through its OpenAI-compatible API.Votes: 0GitHub stars: 32
- Frontier OSS Models 2026--> --- name: frontier-oss-models-2026 description: Work with leading open or openly available model ecosystems from Meta, Mistral, DeepSeek, and xAI. Use when evaluating self-hosted or hybrid deployment paths, model tradeoffs, and integration patterns across non-single-vendor stacks. measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32