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Claude Skills by FreedomIntelligence
github.com/FreedomIntelligence741 skills2 installs1,922 views
- XlsxUse this skill any time a spreadsheet file is the primary input or output. This means any task where the user wants to: open, read, edit, or fix an existing .xlsx, .xlsm, .csv, or .tsv file (e.g., adding columns, computing formulas, formatting, charting, cleaning messy data); create a new spreadsheet from scratch or from other data sources; or convert between tabular file formats. Trigger especially when the user references a spreadsheet file by name or path — even casually (like \"the xlsx i...Votes: 0GitHub stars: 2,984
- Zarr PythonChunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.Votes: 0GitHub stars: 2,984
- Zinc DatabaseAccess ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.Votes: 0GitHub stars: 2,984
- Aav Vector Design Agent--> --- name: 'aav-vector-design-agent' description: 'AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **AAV Vector Design Agent** provides AI-driven design of adeno-associated virus vectors for gene therapy applications. It covers capsid selection a...Votes: 0GitHub stars: 2,984
- AdaptyvCloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing prote...Votes: 0GitHub stars: 2,984
- Adhd Daily PlannerTime-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building systems thatVotes: 0GitHub stars: 2,984
- AeonThis skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.Votes: 0GitHub stars: 2,984
- Agentd Drug Discovery--> --- name: agentd-drug-discovery description: Use the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 2,984
- MAGE--> --- name: mage-antibody-generator description: Ab seq forge keywords: - antibody - antigen - FASTA - generation - validation measurable_outcome: Generate the requested number of antibody sequences (default ≥5) with metadata (model checkpoint, seed) and deliver FASTA files within 10 minutes. license: MIT metadata: author: MAGE Team version: "1.0.0" compatibility: - system: Python 3.9+ / GPU allowed-tools: - run_shell_command - read_file --- Run the MAGE antibody generation workflow to prop...Votes: 0GitHub stars: 2,984
- Antibody Design Agent--> --- name: 'antibody-design-agent' description: 'An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion).' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill brings together cutting-edge tools for antibody engineering, including MAGE (Monoclonal Antibody Generator) and RFdiffusion for Antibodies. It enables the de ...Votes: 0GitHub stars: 2,984
- Armored Cart Design Agent--> --- name: 'armored-cart-design-agent' description: 'AI-powered design of armored CAR-T cells with cytokine/chemokine expression for enhanced solid tumor efficacy, including IL-12, IL-15, IL-18, and IL-7 armoring strategies.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Armored CAR-T Design Agent** provides AI-assisted design of next-generation armored CAR-T cells engineered to express ...Votes: 0GitHub stars: 2,984
- Arxiv SearchSearch arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.Votes: 0GitHub stars: 2,984
- Autonomous Oncology Agent--> --- name: autonomous-oncology-agent description: Precision Oncology keywords: - oncology - multimodal - H&E - biomarkers - NCCN measurable_outcome: Generate a prioritized treatment plan with evidence levels and predicted biomarker status (MSI/KRAS) within 5 minutes of data ingest. license: MIT metadata: author: Nature Cancer 2025 version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - web_fetch --- This skill implements the capabilities of the "Autonomou...Votes: 0GitHub stars: 2,984
- Bayesian Optimizer--> --- name: 'bayesian-optimizer' description: 'Bayesian Optimize' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Bayesian Optimizer** allows agents to efficiently explore a parameter space to maximize a target metric (yield, purity, binding affinity) with minimal experiments. It uses Gaussian Processes to model uncertainty and the Upper Confidence Bound (UCB) acquisition function.Votes: 0GitHub stars: 2,984
- Bgpt Paper SearchSearch scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.Votes: 0GitHub stars: 2,984
- Bindingdb DatabaseQuery BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.Votes: 0GitHub stars: 2,984
- Bio Admet PredictionPredicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxicity endpoints with uncertainty quantification. Filters for PAINS and other structural alerts. Use when filtering compounds for drug-likeness or prioritizing leads by predicted safety.Votes: 0GitHub stars: 2,984
- Bio Alignment Files Bam Statistics--> --- name: bio-alignment-files-bam-statistics description: Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports. tool_type: cli primary_tool: samtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Generate alignment statistics using samtools and pysam.Votes: 0GitHub stars: 2,984
- Bio Alignment Filtering--> --- name: bio-alignment-filtering description: Filter 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. tool_type: cli primary_tool: samtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Filter alignments by flags, quality, and regions using samtools and pysam.Votes: 0GitHub stars: 2,984
- Bio Alignment Indexing--> --- name: bio-alignment-indexing description: Create 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. tool_type: cli primary_tool: samtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Create indices for random access to alignment files using samtools and pysam.Votes: 0GitHub stars: 2,984
- Bio Alignment IoRead, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.Votes: 0GitHub stars: 2,984
- Bio Alignment Msa ParsingParse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.Votes: 0GitHub stars: 2,984
- Bio Alignment Msa StatisticsCalculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.Votes: 0GitHub stars: 2,984
- Bio Alignment PairwisePerform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.Votes: 0GitHub stars: 2,984
- Bio Alignment Sorting--> --- name: bio-alignment-sorting description: Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis. tool_type: cli primary_tool: samtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Sort alignment files by coordinate or read name using samtools and pysam.Votes: 0GitHub stars: 2,984
- Bio Alignment Validation--> --- name: bio-alignment-validation description: Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification. tool_type: mixed primary_tool: samtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Post-alignment quality control to veri...Votes: 0GitHub stars: 2,984
- Bio Atac Seq Atac Peak CallingCall accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.Votes: 0GitHub stars: 2,984
- Bio Atac Seq Atac QcQuality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.Votes: 0GitHub stars: 2,984
- Bio Atac Seq Differential AccessibilityFind differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq experiments.Votes: 0GitHub stars: 2,984
- Bio Atac Seq FootprintingDetect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.Votes: 0GitHub stars: 2,984
- Bio Atac Seq Motif DeviationAnalyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in ATAC-seq data.Votes: 0GitHub stars: 2,984
- Bio Atac Seq Nucleosome PositioningExtract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing nucleosome occupancy patterns from ATAC-seq fragment size distributions.Votes: 0GitHub stars: 2,984
- 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. Guppy is deprecated; use Dorado for all new analyses.Votes: 0GitHub stars: 2,984
- Bio Batch Downloads--> --- name: bio-batch-downloads description: Download large datasets from NCBI efficiently using history server, batching, and rate limiting. Use when performing bulk sequence downloads, handling large query results, or production-scale data retrieval. tool_type: python primary_tool: Bio.Entrez measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Download large numbers of records from NCBI efficiently...Votes: 0GitHub stars: 2,984
- Bio Batch ProcessingProcess multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.Votes: 0GitHub stars: 2,984
- Bio Bedgraph Handling--> --- name: bio-bedgraph-handling description: Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq. tool_type: mixed primary_tool: pyBigWig measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- bedGraph is ...Votes: 0GitHub stars: 2,984
- Bio Blast Searches--> --- name: bio-blast-searches description: Run remote BLAST searches against NCBI databases using Biopython Bio.Blast. Use when identifying unknown sequences, finding homologs, or searching for sequence similarity against NCBI's nr/nt databases. tool_type: python primary_tool: Bio.Blast.NCBIWWW measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Run BLAST searches against NCBI databases using Biopyt...Votes: 0GitHub stars: 2,984
- Bio Causal Genomics Colocalization AnalysisTest whether two traits share a causal variant at a genomic locus using Bayesian colocalization with coloc. Computes posterior probabilities for shared vs distinct causal variants between GWAS and eQTL signals. Use when determining if a GWAS signal and an eQTL share the same causal variant.Votes: 0GitHub stars: 2,984
- Bio Causal Genomics Fine MappingIdentify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.Votes: 0GitHub stars: 2,984
- Bio Causal Genomics Mediation AnalysisDecompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular phenotype mediates the genotype-to-phenotype relationship.Votes: 0GitHub stars: 2,984
- Bio Causal Genomics Mendelian RandomizationEstimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR-Egger, weighted median, and MR-PRESSO methods for robust causal inference from GWAS summary statistics. Use when testing whether an exposure causally affects an outcome using genetic instruments.Votes: 0GitHub stars: 2,984
- Bio Causal Genomics Pleiotropy DetectionDetect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting pleiotropic instruments, or running sensitivity analyses for causal inference.Votes: 0GitHub stars: 2,984
- Bio Cfdna PreprocessingPreprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.Votes: 0GitHub stars: 2,984
- Bio Chipseq Differential BindingDifferential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.Votes: 0GitHub stars: 2,984
- Bio Chipseq Motif AnalysisDe novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.Votes: 0GitHub stars: 2,984
- Bio Chipseq Peak AnnotationAnnotate 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.Votes: 0GitHub stars: 2,984
- Bio Chipseq Peak CallingChIP-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.Votes: 0GitHub stars: 2,984
- Bio Chipseq QcChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.Votes: 0GitHub stars: 2,984
- Bio Chipseq 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: 2,984
- Bio Chipseq VisualizationVisualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.Votes: 0GitHub stars: 2,984