Claude Configs
CLAUDE.md project files and Claude Code slash commands
Showing 8,641–8,700 of 12,603 skills · Page 145 of 211
FreedomIntelligence / bio-alignment-sorting
3.0kSort alignment files by coordinate or read name using samtools and pysam.
FreedomIntelligence / bio-alignment-validation
3.0kPost-alignment quality control to verify alignment quality and identify issues.
FreedomIntelligence / bio-atac-seq-atac-peak-calling
3.0kCall accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters
FreedomIntelligence / bio-atac-seq-differential-accessibility
3.0kFind differentially accessible chromatin regions between conditions using DiffBind or DESeq2
FreedomIntelligence / bio-atac-seq-footprinting
3.0kDetect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS
FreedomIntelligence / bio-atac-seq-motif-deviation
3.0kAnalyze transcription factor motif accessibility variability using chromVAR
FreedomIntelligence / bio-atac-seq-nucleosome-positioning
3.0kExtract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis
FreedomIntelligence / bio-batch-downloads
3.0kDownload large numbers of records from NCBI efficiently using the history server, batching, and proper rate limiting.
FreedomIntelligence / bio-blast-searches
3.0kRun BLAST searches against NCBI databases using Biopython's Bio.Blast module.
FreedomIntelligence / bio-chipseq-super-enhancers
3.0kIdentifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools
FreedomIntelligence / bio-clinical-databases-clinvar-lookup
3.0kQuery ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF
FreedomIntelligence / bio-clinical-databases-gnomad-frequencies
3.0kQuery gnomAD for population allele frequencies to assess variant rarity
FreedomIntelligence / bio-clinical-databases-hla-typing
3.0kCall HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications
FreedomIntelligence / bio-clinical-databases-myvariant-queries
3.0kQuery myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request
FreedomIntelligence / bio-clinical-databases-pharmacogenomics
3.0kQuery PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines
FreedomIntelligence / bio-clinical-databases-polygenic-risk
3.0kCalculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics
FreedomIntelligence / bio-clinical-databases-tumor-mutational-burden
3.0kCalculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds
FreedomIntelligence / bio-clinical-databases-variant-prioritization
3.0kFilter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis
FreedomIntelligence / bio-clip-seq-clip-peak-calling
3.0kPureCLIP uses an HMM to model crosslink sites, incorporating enrichment and truncation signals.
FreedomIntelligence / bio-codon-usage
3.0kAnalyze codon usage patterns and calculate codon adaptation metrics using Biopython.
FreedomIntelligence / bio-compressed-files
3.0kRead and write compressed sequence files (gzip, bzip2, BGZF) using Biopython
FreedomIntelligence / bio-consensus-sequences
3.0kGenerate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus
FreedomIntelligence / bio-copy-number-cnv-annotation
3.0kAnnotate CNVs with genes, pathways, and clinical significance
FreedomIntelligence / bio-crispr-screens-jacks-analysis
3.0kJACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality
FreedomIntelligence / bio-data-visualization-circos-plots
3.0kCircular genome visualizations for displaying multiple data tracks around chromosome ideograms.
FreedomIntelligence / bio-entrez-fetch
3.0kRetrieve records from NCBI databases using Biopython's Entrez module (EFetch, ESummary utilities).
FreedomIntelligence / bio-entrez-link
3.0kNavigate between NCBI databases using Biopython's Entrez module (ELink utility).
FreedomIntelligence / bio-entrez-search
3.0kSearch NCBI databases using Biopython's Entrez module (ESearch, EInfo, EGQuery utilities).
FreedomIntelligence / bio-filter-sequences
3.0kFilter and select sequences by criteria (length, ID, GC content, patterns) using Biopython
FreedomIntelligence / bio-flow-cytometry-compensation-transformation
3.0kSpillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms
FreedomIntelligence / bio-flow-cytometry-differential-analysis
3.0kDifferential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods
FreedomIntelligence / bio-flow-cytometry-fcs-handling
3.0kRead and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration
FreedomIntelligence / bio-flow-cytometry-gating-analysis
3.0kManual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates
FreedomIntelligence / bio-genome-assembly-assembly-polishing
3.0kImprove assembly accuracy by correcting errors using additional sequencing data.
FreedomIntelligence / bio-genome-assembly-assembly-qc
3.0kEvaluate genome assembly quality with contiguity metrics (QUAST) and gene completeness (BUSCO).
FreedomIntelligence / bio-genome-assembly-long-read-assembly
3.0kAssemble genomes from Oxford Nanopore (ONT) or PacBio long reads for highly contiguous assemblies.
FreedomIntelligence / bio-genome-assembly-short-read-assembly
3.0kAssemble genomes from Illumina paired-end or single-end reads using SPAdes.
FreedomIntelligence / bio-genome-intervals-bed-file-basics
3.0kBED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates.
FreedomIntelligence / bio-genome-intervals-bigwig-tracks
3.0kBigWig is an indexed binary format for continuous genomic data. Efficient for genome browsers and programmatic access.
FreedomIntelligence / bio-genome-intervals-coverage-analysis
3.0kCalculate coverage and depth across genomic regions using bedtools and pybedtools.
FreedomIntelligence / bio-genome-intervals-gtf-gff-handling
3.0kGTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates.
FreedomIntelligence / bio-genome-intervals-interval-arithmetic
3.0kCore set operations on genomic intervals using bedtools (CLI) and pybedtools (Python).
FreedomIntelligence / bio-genome-intervals-proximity-operations
3.0kOperations for finding nearby features and extending intervals using bedtools and pybedtools.
FreedomIntelligence / bio-geo-data
3.0kQuery and access Gene Expression Omnibus datasets using Biopython's Entrez module.
FreedomIntelligence / bio-imaging-mass-cytometry-quality-metrics
3.0kQuality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC
FreedomIntelligence / bio-isoform-switching
3.0kAnalyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential shifts between conditions
FreedomIntelligence / bio-liquid-biopsy-pipeline
3.0kComplete workflow for cfDNA analysis from sequencing to clinical interpretation.
FreedomIntelligence / bio-local-blast
3.0kRun BLAST searches locally using NCBI BLAST+ command-line tools.
FreedomIntelligence / bio-long-read-sequencing-clair3-variants
3.0kDeep learning-based variant calling from long reads using Clair3 for SNPs and small indels
FreedomIntelligence / bio-long-read-sequencing-isoseq-analysis
3.0kAnalyze PacBio Iso-Seq data for full-length isoform discovery and quantification
cloudflare / cloudflare
2.9kDiscover and choose Cloudflare products for apps, APIs, AI agents, storage, networking, and security. Use for architecture and product selection, including when the user describes a need without naming a Cloudflare product; then find the relevant skill or documentation.
tradermonty / parabolic-short-trade-planner
2.9kScreen US equities for parabolic exhaustion patterns and generate conditional pre-market short plans, then evaluate intraday trigger fires from live 5-min bars.
tradermonty / us-stock-analysis
2.9kComprehensive US stock analysis including fundamental analysis (financial metrics, business quality, valuation), technical analysis (indicators, chart patterns, support/resistance), stock comparisons, and investment report generation
mikubaka88 / ccf-idea-optimizer
2.8kDevelop and optimize rough CCF research ideas into problems, insights, mechanisms, and evidence plans. Use for 优化idea, 具象化idea, 找方向, 方向探索, and rescue routes when development is the requested deliverable.
mikubaka88 / ccf-idea-reviewer
2.8kAssess research ideas for value, novelty, insight, and mechanism. Use for 思路审核, 靠谱吗, 值得做吗, 创新够不够, idea review, scoring, and ranking; no numeric-score request is needed. Default to concept-only review without experiment assessment, including ideas extracted from manuscripts.
mikubaka88 / ccf-paper-writer
2.8kDraft, revise, polish, compress, or presentation-adapt CCF manuscript prose. Use for 写作, 润色论文, research documents to complete papers, 完整初稿, 实验留空, 改写, 压缩论文, abstracts, sections, and slides. Draft content before fitting pages; preserve evidence and format.
mikubaka88 / ccf-visual-composer
2.8kRender and redesign scientific figures, visual tables, and method/architecture diagrams from supplied content, including biological data. Use for 绘图美化, 排版, 配色, GPT Image 2 generation, pure SVG, and editable SVG/PDF/PPTX. Preserve values and topology.
Nanako0129 / sepia
2.8kMake AI-generated writing read as human-written, in fiction and in professional prose. Repairs the narrative architecture of fiction and stories (based on StoryScope, arXiv:2604.03136); routes professional text through domain rules for release notes, announcements, PR and issue replies, code-review…
elementalsouls / cloud-saas-exposure
2.7kOrganization-grade cloud and supply-chain attack-surface discovery: S3/GCS/Azure Blob bucket discovery via observed-name mining (CNAME/cert-SAN/Wayback) and bounded two-class permutation (6 prefixes x 15 suffixes on trusted tokens, bounded target-bound expansion on subdomain stems), existence (HEAD/…
elementalsouls / continuous-exposure-monitoring
2.7kTurns one-shot external recon into a continuous monitoring program. Covers the scheduled re-scan-and-diff loop (baseline snapshot -> interval sleep -> re-scan -> asset/finding delta -> threshold-gated webhook alert), the scan-to-scan diff engine (new/removed/changed assets by a tracked-attribute tab…