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Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,578 skills3 installs3,530 views
- Peak Annotation--> --- name: bio-chipseq-peak-annotation description: Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation plots and statistics. Use when annotating ChIP-seq peaks to genomic features. tool_type: r primary_tool: ChIPseeker measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_fi...Votes: 0GitHub stars: 6
- Peak Calling--> --- name: bio-chipseq-peak-calling description: ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use when calling peaks from ChIP-seq alignments. tool_type: cli primary_tool: macs3 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: ...Votes: 0GitHub stars: 6
- Super Enhancers--> --- name: bio-chipseq-super-enhancers description: Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains. tool_type: cli primary_tool: ROSE measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Identify supe...Votes: 0GitHub stars: 6
- Binding Site Annotation--> --- name: bio-clip-seq-binding-site-annotation description: Annotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts. tool_type: mixed primary_tool: ChIPseeker measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Clip Alignment--> --- name: bio-clip-seq-clip-alignment description: Align CLIP-seq reads to the genome with crosslink site awareness. Use when mapping preprocessed CLIP reads for peak calling. tool_type: cli primary_tool: STAR measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Clip Motif Analysis--> --- name: bio-clip-seq-clip-motif-analysis description: Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein. tool_type: cli primary_tool: HOMER measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Clip Peak Calling--> --- name: bio-clip-seq-clip-peak-calling description: Call protein-RNA binding site peaks from CLIP-seq data using CLIPper, PureCLIP, or Piranha. Use when identifying RBP binding sites from aligned CLIP reads. tool_type: cli primary_tool: CLIPper measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Clip Preprocessing--> --- name: bio-clip-seq-clip-preprocessing description: Preprocess CLIP-seq data including adapter trimming, UMI extraction, and PCR duplicate removal. Use when preparing raw CLIP, iCLIP, or eCLIP reads for peak calling. tool_type: cli primary_tool: umi_tools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- M6a Differential--> --- name: bio-epitranscriptomics-m6a-differential description: Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or cell states. tool_type: r primary_tool: exomePeak2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- M6a Peak Calling--> --- name: bio-epitranscriptomics-m6a-peak-calling description: Call m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data. tool_type: mixed primary_tool: exomePeak2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- M6anet Analysis--> --- name: bio-epitranscriptomics-m6anet-analysis description: Detect m6A modifications from Oxford Nanopore direct RNA sequencing using m6Anet. Use when analyzing epitranscriptomic modifications from long-read RNA data without immunoprecipitation. tool_type: python primary_tool: m6Anet measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Documentation: https://m6anet.readthedocs.io/Votes: 0GitHub stars: 6
- Merip Preprocessing--> --- name: bio-epitranscriptomics-merip-preprocessing description: Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis. tool_type: cli primary_tool: STAR measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Modification Visualization--> --- name: bio-epitranscriptomics-modification-visualization description: Create metagene plots and browser tracks for RNA modification data. Use when visualizing m6A distribution patterns around genomic features like stop codons. tool_type: r primary_tool: Guitar measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Bismark Alignment--> --- name: bio-methylation-bismark-alignment description: Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome. tool_type: cli primary_tool: bismark measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Dmr Detection--> --- name: bio-methylation-dmr-detection description: Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions or cell types. tool_type: r primary_tool: methylKit measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Methylation Calling--> --- name: bio-methylation-calling description: Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite sequencing data for downstream analysis. tool_type: cli primary_tool: bismark measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Methylkit Analysis--> --- name: bio-methylation-methylkit description: DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR detection. tool_type: r primary_tool: methylKit measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Batch Design--> --- name: bio-experimental-design-batch-design description: Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals. tool_type: r primary_tool: sva measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_sh...Votes: 0GitHub stars: 6
- Multiple Testing--> --- name: bio-experimental-design-multiple-testing description: Applies multiple testing correction methods including FDR, Bonferroni, and q-value for genomics data. Use when filtering differential expression results, setting significance thresholds, or choosing between correction methods for different study designs. tool_type: r primary_tool: qvalue measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Power Analysis--> --- name: bio-experimental-design-power-analysis description: Calculates statistical power and minimum sample sizes for RNA-seq, ATAC-seq, and other sequencing experiments. Use when planning experiments, determining how many replicates are needed, or assessing whether a study is adequately powered to detect expected effect sizes. tool_type: r primary_tool: RNASeqPower measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - ...Votes: 0GitHub stars: 6
- Sample Size--> --- name: bio-experimental-design-sample-size description: Estimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies. Use when budgeting experiments, writing grant proposals, or determining minimum replicates needed to achieve statistical significance for expected effect sizes. tool_type: r primary_tool: ssizeRNA measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_she...Votes: 0GitHub stars: 6
- Clinical Trial Matcher--> --- name: 'clinical-trial-matcher' description: 'Matches patient profiles to open clinical trials using vector similarity and inclusion/exclusion criteria. Use when a user provides patient data and asks for relevant trials.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill matches a patient's clinical profile against a database of active clinical trials (ClinicalTrials.gov).Votes: 0GitHub stars: 6
- Crispr Designer--> --- name: 'crispr-designer' description: 'Designs guide RNA (gRNA) sequences for CRISPR-Cas9 editing, including off-target analysis. Use when a user needs to edit a gene or asks for gRNA sequences.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill designs high-efficiency guide RNAs for gene editing experiments.Votes: 0GitHub stars: 6
- Regulatory Drafter--> --- name: 'regulatory-drafter' description: 'Drafts regulatory documents (FDA, EMA) with audit trails and specific "Thinking Block" reasoning. Use for high-stakes compliance writing.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill generates compliant drafts for regulatory submissions, emphasizing auditability and adherence to guidelines (ICH, FDA).Votes: 0GitHub stars: 6
- Algorithmic Art--> --- name: 'algorithmic-art' description: 'Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists'' work to avoid copyright violations.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - ru...Votes: 0GitHub stars: 6
- Brand Guidelines--> --- name: 'brand-guidelines' description: 'Applies Anthropic''s official brand colors and typography to any sort of artifact that may benefit from having Anthropic''s look-and-feel. Use it when brand colors or style guidelines, visual formatting, or company design standards apply.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Canvas Design--> --- name: 'canvas-design' description: 'Create beautiful visual art in .png and .pdf documents using design philosophy. You should use this skill when the user asks to create a poster, piece of art, design, or other static piece. Create original visual designs, never copying existing artists'' work to avoid copyright violations.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- These are instruc...Votes: 0GitHub stars: 6
- Doc Coauthoring--> --- name: 'doc-coauthoring' description: 'Guide users through a structured workflow for co-authoring documentation. Use when user wants to write documentation, proposals, technical specs, decision docs, or similar structured content. This workflow helps users efficiently transfer context, refine content through iteration, and verify the doc works for readers. Trigger when user mentions writing docs, creating proposals, drafting specs, or similar documentation tasks.' measurable_outcome: E...Votes: 0GitHub stars: 6
- Docx--> --- name: 'docx' description: '"Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction. When Claude needs to work with professional documents (.docx files) for: (1) Creating new documents, (2) Modifying or editing content, (3) Working with tracked changes, (4) Adding comments, or any other document tasks"' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. all...Votes: 0GitHub stars: 6
- Frontend Design--> --- name: 'frontend-design' description: 'Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, artifacts, posters, or applications (examples include websites, landing pages, dashboards, React components, HTML/CSS layouts, or when styling/beautifying any web UI). Generates creative, polished code and UI design that avoids generic AI aesthetics.' measurable_outcome: Execute skill workflow success...Votes: 0GitHub stars: 6
- Internal Comms--> --- name: 'internal-comms' description: 'A set of resources to help me write all kinds of internal communications, using the formats that my company likes to use. Claude should use this skill whenever asked to write some sort of internal communications (status reports, leadership updates, 3P updates, company newsletters, FAQs, incident reports, project updates, etc.).' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file -...Votes: 0GitHub stars: 6
- Mcp Builder--> --- name: 'mcp-builder' description: 'Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Pdf--> --- name: 'pdf' description: 'Comprehensive PDF manipulation toolkit for extracting text and tables, creating new PDFs, merging/splitting documents, and handling forms. When Claude needs to fill in a PDF form or programmatically process, generate, or analyze PDF documents at scale.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Pptx--> --- name: 'pptx' description: '"Presentation creation, editing, and analysis. When Claude needs to work with presentations (.pptx files) for: (1) Creating new presentations, (2) Modifying or editing content, (3) Working with layouts, (4) Adding comments or speaker notes, or any other presentation tasks"' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Skill Creator--> --- name: 'skill-creator' description: 'Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Claude''s capabilities with specialized knowledge, workflows, or tool integrations.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill provides guidance for creating effective skills.Votes: 0GitHub stars: 6
- Slack Gif Creator--> --- name: 'slack-gif-creator' description: 'Knowledge and utilities for creating animated GIFs optimized for Slack. Provides constraints, validation tools, and animation concepts. Use when users request animated GIFs for Slack like "make me a GIF of X doing Y for Slack."' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- A toolkit providing utilities and knowledge for creating animated GIFs optim...Votes: 0GitHub stars: 6
- Theme Factory--> --- name: 'theme-factory' description: 'Toolkit for styling artifacts with a theme. These artifacts can be slides, docs, reportings, HTML landing pages, etc. There are 10 pre-set themes with colors/fonts that you can apply to any artifact that has been creating, or can generate a new theme on-the-fly.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill provides a curated collection of p...Votes: 0GitHub stars: 6
- Web Artifacts Builder--> --- name: 'web-artifacts-builder' description: 'Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologies (React, Tailwind CSS, shadcn/ui). Use for complex artifacts requiring state management, routing, or shadcn/ui components - not for simple single-file HTML/JSX artifacts.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- To build po...Votes: 0GitHub stars: 6
- Webapp Testing--> --- name: 'webapp-testing' description: 'Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- To test local web applications, write native Python Playwright scripts. **Helper Scripts Available**: ...Votes: 0GitHub stars: 6
- Xlsx--> --- name: 'xlsx' description: '"Comprehensive spreadsheet creation, editing, and analysis with support for formulas, formatting, data analysis, and visualization. When Claude needs to work with spreadsheets (.xlsx, .xlsm, .csv, .tsv, etc) for: (1) Creating new spreadsheets with formulas and formatting, (2) Reading or analyzing data, (3) Modify existing spreadsheets while preserving formulas, (4) Data analysis and visualization in spreadsheets, or (5) Recalculating formulas"' measurable_ou...Votes: 0GitHub stars: 6
- Template--> --- name: 'template-skill' description: 'Replace with description of the skill and when Claude should use it.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->Votes: 0GitHub stars: 6
- Gh Address Comments--> ---name: gh-address-comments description: Help address review/issue comments on the open GitHub PR for the current branch using gh CLI; verify gh auth first and prompt the user to authenticate if not logged in. metadata: short-description: Address comments in a GitHub PR review keywords: - gh-address-comments - automation - biomedical measurable_outcome: execute task with >95% success rate. allowed-tools: - read_file - run_shell_command ---" Guide to find the open PR for the current branc...Votes: 0GitHub stars: 6
- Gh Fix Ci--> ---name: gh-fix-ci description: Inspect GitHub PR checks with gh, pull failing GitHub Actions logs, summarize failure context, then create a fix plan and implement after user approval. Use when a user asks to debug or fix failing PR CI/CD checks on GitHub Actions and wants a plan + code changes; for external checks (e.g., Buildkite), only report the details URL and mark them out of scope. metadata: short-description: Fix failing Github CI actions keywords: - gh-fix-ci - automation - biome...Votes: 0GitHub stars: 6
- Notion Knowledge Capture--> ---name: notion-knowledge-capture description: Capture conversations and decisions into structured Notion pages; use when turning chats/notes into wiki entries, how-tos, decisions, or FAQs with proper linking. metadata: short-description: Capture conversations into structured Notion pages keywords: - notion-knowledge-capture - automation - biomedical measurable_outcome: execute task with >95% success rate. allowed-tools: - read_file - run_shell_command ---" Convert conversations and notes...Votes: 0GitHub stars: 6
- Notion Meeting Intelligence--> ---name: notion-meeting-intelligence description: Prepare meeting materials with Notion context and Codex research; use when gathering context, drafting agendas/pre-reads, and tailoring materials to attendees. metadata: short-description: Prep meetings with Notion context and tailored agendas keywords: - notion-meeting-intelligence - automation - biomedical measurable_outcome: execute task with >95% success rate. allowed-tools: - read_file - run_shell_command ---" Prep meetings by pulling...Votes: 0GitHub stars: 6
- Notion Research Documentation--> ---name: notion-research-documentation description: Research across Notion and synthesize into structured documentation; use when gathering info from multiple Notion sources to produce briefs, comparisons, or reports with citations. metadata: short-description: Research Notion content and produce briefs/reports keywords: - notion-research-documentation - automation - biomedical measurable_outcome: execute task with >95% success rate. allowed-tools: - read_file - run_shell_command ---" Pul...Votes: 0GitHub stars: 6
- Notion Spec To Implementation--> ---name: notion-spec-to-implementation description: Turn Notion specs into implementation plans, tasks, and progress tracking; use when implementing PRDs/feature specs and creating Notion plans + tasks from them. metadata: short-description: Turn Notion specs into implementation plans, tasks, and progress tracking keywords: - notion-spec-to-implementation - automation - biomedical measurable_outcome: execute task with >95% success rate. allowed-tools: - read_file - run_shell_command ---" ...Votes: 0GitHub stars: 6
- Create Plan--> ---name: create-plan description: Create a concise plan. Use when a user explicitly asks for a plan related to a coding task. metadata: short-description: Create a plan keywords: - create-plan - automation - biomedical measurable_outcome: execute task with >95% success rate. allowed-tools: - read_file - run_shell_command ---"Votes: 0GitHub stars: 6
- Linear--> ---name: linear description: Manage issues, projects & team workflows in Linear. Use when the user wants to read, create or updates tickets in Linear. metadata: short-description: Manage Linear issues in Codex keywords: - linear - automation - biomedical measurable_outcome: execute task with >95% success rate. allowed-tools: - read_file - run_shell_command ---"Votes: 0GitHub stars: 6
- Skill Creator--> ---name: skill-creator description: Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with specialized knowledge, workflows, or tool integrations. metadata: short-description: Create or update a skill keywords: - skill-creator - automation - biomedical measurable_outcome: execute task with >95% success rate. allowed-tools: - read_file - run_shell_command ---" This skill provi...Votes: 0GitHub stars: 6