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Claude Skills by GPTomics
github.com/GPTomics537 skills2 installs584 views
- 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: 1,198
- 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: 1,198
- 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: 1,198
- Alignment ValidationValidate 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.Votes: 0GitHub stars: 1,198
- Bam StatisticsGenerate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.Votes: 0GitHub stars: 1,198
- 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: 1,198
- Pileup GenerationGenerate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.Votes: 0GitHub stars: 1,198
- Reference OperationsGenerate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.Votes: 0GitHub stars: 1,198
- Sam Bam BasicsView, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.Votes: 0GitHub stars: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- Pairwise AlignmentPerform 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: 1,198
- Differential SplicingDetects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes. Use when comparing splicing patterns between treatment groups, tissues, or disease states.Votes: 0GitHub stars: 1,198
- Isoform SwitchingAnalyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential shifts between conditions. Use when investigating how splicing changes affect protein function.Votes: 0GitHub stars: 1,198
- Sashimi PlotsCreates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot. Visualizes differential splicing events with grouped samples and junction read support. Use when visualizing specific splicing events or validating differential splicing results.Votes: 0GitHub stars: 1,198
- Single Cell SplicingAnalyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection. Identifies cell-type-specific splicing patterns. Use when analyzing isoform usage in scRNA-seq or finding splicing differences between cell populations.Votes: 0GitHub stars: 1,198
- Splicing QcAssesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC. Use when evaluating data suitability for splicing analysis or troubleshooting low event detection.Votes: 0GitHub stars: 1,198
- Splicing QuantificationQuantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files. Calculates inclusion levels for skipped exons, alternative splice sites, mutually exclusive exons, and retained introns. Use when measuring splice site usage or isoform ratios from RNA-seq data.Votes: 0GitHub stars: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- Molecular DescriptorsCalculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filtering by drug-likeness criteria.Votes: 0GitHub stars: 1,198
- Molecular IoReads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.Votes: 0GitHub stars: 1,198
- Reaction EnumerationEnumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with product validation. Use when creating combinatorial libraries or enumerating products from synthetic routes.Votes: 0GitHub stars: 1,198
- Similarity SearchingPerforms molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit. Finds structurally similar compounds using ECFP or MACCS keys and clusters molecules by structural similarity using Butina clustering. Use when finding analogs of a query compound or clustering chemical libraries.Votes: 0GitHub stars: 1,198
- Substructure SearchSearches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.Votes: 0GitHub stars: 1,198
- Virtual ScreeningPerforms structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes, and ranks compounds by predicted binding affinity. Use when screening chemical libraries against a protein structure to find potential binders.Votes: 0GitHub stars: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- 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: 1,198
- Clinvar LookupQuery ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.Votes: 0GitHub stars: 1,198
- Dbsnp QueriesQuery dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.Votes: 0GitHub stars: 1,198
- Gnomad FrequenciesQuery gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequency for rare disease analysis or determining if a variant is common in the general population.Votes: 0GitHub stars: 1,198
- Hla TypingCall HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.Votes: 0GitHub stars: 1,198
- Myvariant QueriesQuery myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request. Use when annotating variants with clinical and population data from multiple sources simultaneously.Votes: 0GitHub stars: 1,198
- PharmacogenomicsQuery PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines. Use when predicting drug response from genetic variants or implementing clinical pharmacogenomics.Votes: 0GitHub stars: 1,198