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Tools & Automation
CLI tools, utilities, converters, workflow automation, and productivity helpers
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Showing 2,641–2,664 of 46,837 skills
- Bio Epitranscriptomics Merip PreprocessingAlign and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.Votes: 0GitHub stars: 2
- Bio Epitranscriptomics M6a Peak CallingCall m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data.Votes: 0GitHub stars: 2
- Bio Duplicate HandlingMark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.Votes: 0GitHub stars: 2
- Bio Consensus SequencesGenerate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.Votes: 0GitHub stars: 2
- Bio Clip Seq Clip PreprocessingPreprocess CLIP-seq data including adapter trimming, UMI extraction, and PCR duplicate removal. Use when preparing raw CLIP, iCLIP, or eCLIP reads for peak calling.Votes: 0GitHub stars: 2
- Bio Clip Seq Clip Motif AnalysisIdentify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.Votes: 0GitHub stars: 2
- Bio Clip Seq Clip AlignmentAlign CLIP-seq reads to the genome with crosslink site awareness. Use when mapping preprocessed CLIP reads for peak calling.Votes: 0GitHub stars: 2
- Bio Clip Seq Binding Site AnnotationAnnotate 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.Votes: 0GitHub stars: 2
- Bio Chip Seq Super EnhancersIdentifies 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.Votes: 0GitHub stars: 2
- Bio BasecallingConvert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new analyses.Votes: 0GitHub stars: 2
- Bio Alignment Statistics 1Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.Votes: 0GitHub stars: 2
- Bio Alignment SortingSort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.Votes: 0GitHub stars: 2
- Bio Alignment IndexingCreate and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.Votes: 0GitHub stars: 2
- Bio Alignment FilteringFilter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.Votes: 0GitHub stars: 2
- Big ReviewRun the local `review.sh` script to get multi-model review findings, then triage and address valid issues before final validation and PR creation.Votes: 0GitHub stars: 2
- Better ContextClone and explore external codebases using the better-context CLI. Use this skill when: - User wants to explore a GitHub repository (e.g., "explore anthropics/claude-code") - User asks how a library/framework works and you need to read its source - User wants to understand implementation details of an external project - User provides a repo URL or owner/repo and wants you to examine itVotes: 0GitHub stars: 2
- BenchmarkRun benchmarks for the crypto-rs-backtester project (Python and Rust).Votes: 0GitHub stars: 2
- Bear Notes 1Create, search, and manage Bear notes via grizzly CLI.Votes: 0GitHub stars: 2
- Beans Issue TrackingTracks work with beans CLI for audit trails and agent memory. Use when starting tasks, finding next work, or recording discovered issues during implementation.Votes: 0GitHub stars: 2
- Beads WorkflowBeads issue tracking and workflow management with automatic git branch creation. MUST BE USED for Beads operations. Handles full epic→branch→work lifecycle, dependencies, and ready task queries. Use when creating epics/features (auto-creates branch), tracking work, finding ready issues, or managing dependencies, or when user mentions "create issue", "track work", "bd create", "find ready tasks", issue management, dependencies, work tracking, or Beads workflow operations.Votes: 0GitHub stars: 2
- Beads ReviewReview, proofread, refine, and polish existing Beads epics and issues for clarity, completeness, and smooth implementation. Use after Beads have been filed, or when asked to audit/improve a Beads tracker.Votes: 0GitHub stars: 2
- Beads Issue TrackingUse this when working on tasks in this repo that require bd (beads) issue tracking, status updates, and the mandatory end-of-session push workflow.Votes: 0GitHub stars: 2
- Beads ImplementImplement Beads work items from a bead id. Use when the user runs $beads-implement <bead-id> or asks to implement a bead/epic; if it is an epic, implement all sub-tasks, committing after each one and only interrupting when blocked or a decision is needed.Votes: 0GitHub stars: 2
- Beads CreateTranslate a finalized plan into Beads epics and issues with clear dependencies, design notes, and parallelization. Use when asked to file Beads from a plan/spec (OpenSpec, PRD, design doc), or when converting an external plan into a detailed Beads tracking structure.Votes: 0GitHub stars: 2