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Claude Skills by BioTender-max
github.com/BioTender-max897 skills8 installs817 views
- Adaptive DesignsDesigns adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size...Votes: 0GitHub stars: 171
- Admet PredictionPredicts ADMET properties using ADMETlab 3.0 (119 endpoints with uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES gold-standard endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.Votes: 0GitHub stars: 171
- Ago Clip Mirna TargetsIdentify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recov...Votes: 0GitHub stars: 171
- Alignment Amplicon ClippingTrim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.Votes: 0GitHub stars: 171
- 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: 171
- Alignment Free QuantQuantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.Votes: 0GitHub stars: 171
- 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: 171
- 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: 171
- 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: 171
- Alignment TrimmingTrim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.Votes: 0GitHub stars: 171
- 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: 171
- Allele Specific AccessibilityDetect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.Votes: 0GitHub stars: 171
- Allele Specific BindingDetects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying...Votes: 0GitHub stars: 171
- Allele Specific Copy NumberInfer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than rel...Votes: 0GitHub stars: 171
- Ancestral ReconstructionReconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs...Votes: 0GitHub stars: 171
- Annotation TransferTransfer gene annotations between genome assemblies using Liftoff for same-species annotation liftover and MiniProt for cross-species protein-to-genome alignment. Enables rapid annotation of new assemblies using existing reference annotations. Use when annotating a new assembly of a species with an existing reference annotation or mapping annotations across related species.Votes: 0GitHub stars: 171
- Assembly PolishingPolish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools.Votes: 0GitHub stars: 171
- Assembly QcAssess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality.Votes: 0GitHub stars: 171
- Association TestingGenome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result visualization. Use when running GWAS or association tests.Votes: 0GitHub stars: 171
- Atac Peak CallingCall accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.Votes: 0GitHub stars: 171
- Atac QcATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.Votes: 0GitHub stars: 171
- Atacseq PipelineEnd-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting. Use when running end-to-end ATAC-seq analysis from FASTQ to differential accessibility.Votes: 0GitHub stars: 171
- Atlas MappingMaps query single-cell data to reference atlases using scArches transfer learning with scVI and scANVI models. Transfers cell type labels without retraining on combined data. Use when annotating new single-cell datasets using pre-trained reference models.Votes: 0GitHub stars: 171
- Automated Qc ReportsGenerates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.Votes: 0GitHub stars: 171
- Bagel EssentialityIdentifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 ...Votes: 0GitHub stars: 171
- Bam StatisticsGenerate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.Votes: 0GitHub stars: 171
- Base Editing AnalysisAnalyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation ag...Votes: 0GitHub stars: 171
- 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: 171
- Batch CorrectionBatch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect fo...Votes: 0GitHub stars: 171
- Batch DesignDesigns experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals.Votes: 0GitHub stars: 171
- Batch DownloadsDownload large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.Votes: 0GitHub stars: 171
- Bayesian InferenceRun Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison. Use when needing posterior probability support, Bayesian model averaging, site-heterogeneous models for deep phylogenies, or formal model comparison via stepping-stone sampling.Votes: 0GitHub stars: 171
- Bayesian TrialsDesigns Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and posterior probability stopping rules. Covers FDA Bayesian Devices Guidance (2010), FDA Bayesian Methodology in Drugs Draft (January 2026), BOIN Fit-for-Purpose qualification (Decembe...Votes: 0GitHub stars: 171
- Bed File BasicsBED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and pybedtools. Use when working with genomic coordinates or preparing interval files for downstream tools.Votes: 0GitHub stars: 171
- Bedgraph HandlingCreate, 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.Votes: 0GitHub stars: 171
- Bigwig TracksCreate and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions.Votes: 0GitHub stars: 171
- Binding Site AnnotationAnnotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, o...Votes: 0GitHub stars: 171
- Biodiversity MetricsCalculates species richness, diversity, and turnover using the Hill number framework with iNEXT coverage-based rarefaction/extrapolation, asymptotic diversity estimation, and beta diversity partitioning (betapart turnover vs nestedness). Compares assemblages using coverage-standardized rather than size-standardized rarefaction. Use when quantifying biodiversity from species abundance or incidence data, comparing diversity across sites, or constructing rarefaction curves. Not for clinical 16S ...Votes: 0GitHub stars: 171
- Biomarker DiscoverySelects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization. Use when identifying biomarkers from high-dimensional omics data.Votes: 0GitHub stars: 171
- Biomarker PipelineEnd-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, classifier training with nested CV, and SHAP interpretation. Use when building and validating diagnostic or prognostic biomarker signatures from omics data.Votes: 0GitHub stars: 171
- Biomart QueriesBulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hiera...Votes: 0GitHub stars: 171
- Bioskills InstallerInstalls 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.Votes: 0GitHub stars: 171
- Bioskills Database Access Ortholog InferencePull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and w...Votes: 0GitHub stars: 171
- Bioskills Differential Expression Batch CorrectionRemove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting batch effects in expression data.Votes: 0GitHub stars: 171
- Bioskills Machine Learning Survival AnalysisAnalyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival models from clinical and omics features. Use when predicting patient survival or modeling time-to-event outcomes.Votes: 0GitHub stars: 171
- Bioskills Proteomics Differential AbundanceStatistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and DEqMS workflows with empirical Bayes moderation, fold change shrinkage for accurate effect size estimation, and Python alternatives. Use when identifying proteins with significant abundance changes between experimental groups.Votes: 0GitHub stars: 171
- Bioskills Restriction Analysis Fragment AnalysisAnalyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns.Votes: 0GitHub stars: 171
- Bismark AlignmentBisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.Votes: 0GitHub stars: 171
- Blast SearchesRun remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS tax...Votes: 0GitHub stars: 171
- Bowtie2 AlignmentAlign short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.Votes: 0GitHub stars: 171