Browse Secure Claude Skills
Search verified agent skills and review security grades before installing · full A–Z index
- PaperBananaAgentic framework for automating the generation of publication-ready academic illustrations and statistical plots.Votes: 0GitHub stars: 32
- Dia AnalysisData-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.Votes: 0GitHub stars: 32
- Plink BasicsPLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 and 2.0. Use when working with PLINK format files or running QC.Votes: 0GitHub stars: 32
- Tree IoRead, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, or handling multiple trees.Votes: 0GitHub stars: 32
- Drug InteractionChecks for potential drug-drug interactions (DDIs) between a list of medications.Votes: 0GitHub stars: 32
- Umi ProcessingExtract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.Votes: 0GitHub stars: 32
- Quality ReportsGenerate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresented sequences. Use when performing initial QC on raw sequencing data or validating preprocessing results.Votes: 0GitHub stars: 32
- Quality FilteringFilter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard reads below thresholds. Use when reads have poor quality tails or require minimum quality for downstream analysis.Votes: 0GitHub stars: 32
- Contamination ScreeningDetect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting cross-contamination or working with samples prone to microbial contamination.Votes: 0GitHub stars: 32
- Star AlignmentAlign RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery. Use when aligning RNA-seq data requiring splice-aware alignment.Votes: 0GitHub stars: 32
- Qiime2 WorkflowQIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.Votes: 0GitHub stars: 32
- Xcms PreprocessingXCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for untargeted metabolomics.Votes: 0GitHub stars: 32
- Linear AlgebraTensor OperationsVotes: 0GitHub stars: 32
- Reference PanelsDownload, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels for target populations.Votes: 0GitHub stars: 32
- Structural VariantsDetect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.Votes: 0GitHub stars: 32
- Medaka PolishingPolish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore data without short-read polishing.Votes: 0GitHub stars: 32
- Long Read AlignmentAlign long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis.Votes: 0GitHub stars: 32
- Off Target PredictionPredict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity. Use when evaluating guide RNA specificity or selecting guides with minimal off-target risk.Votes: 0GitHub stars: 32
- Hdr Template DesignDesign homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms. Use when designing donor templates for precise insertions, tagging, or allele replacement.Votes: 0GitHub stars: 32
- Short Read AssemblyDe novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly modes. Use when assembling genomes from Illumina reads.Votes: 0GitHub stars: 32