smithery/gptomics

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bio-data-visualization-genome-tracks Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screensho…

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bio-data-visualization-heatmaps-clustering Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/sc…

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bio-data-visualization-interactive-visualization Build interactive HTML/web visualizations with plotly (Python/R), bokeh (Python), and gganimate/plotly frames for ani…

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bio-data-visualization-multipanel-figures Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Py…

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bio-data-visualization-upset-plots Build UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern, ggplot2…

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bio-differential-expression-batch-correction Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for vi…

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bio-differential-expression-de-results Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling o…

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bio-differential-expression-de-visualization Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot…

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bio-differential-expression-deseq2-basics Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing…

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bio-differential-expression-edger-basics Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F…

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bio-differential-expression-timeseries-de Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT…

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bio-duplicate-handling Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant …

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bio-entrez-fetch Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary).

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bio-entrez-link Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink).

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bio-entrez-search Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell).

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bio-epitranscriptomics-m6a-differential Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-b…

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bio-epitranscriptomics-m6a-peak-calling Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-correcte…

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bio-epitranscriptomics-m6anet-analysis Detects m6A modifications from Oxford Nanopore direct-RNA-seq (DRS) signal using m6Anet (multiple-instance-learning o…

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bio-epitranscriptomics-merip-preprocessing Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splic…

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bio-epitranscriptomics-modification-visualization Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools comp…

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bio-experimental-design-batch-design Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, p…

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bio-experimental-design-multiple-testing Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods …

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bio-experimental-design-power-analysis Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, …

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bio-experimental-design-sample-size Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experime…

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bio-expression-matrix-counts-ingest Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or …

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bio-expression-matrix-gene-id-mapping Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, bioma…

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bio-expression-matrix-sparse-handling Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatri…

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bio-fastq-quality Work with FASTQ quality scores using Biopython - access Phred scores, filter and trim by quality, compute per-positio…

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bio-filter-sequences Filter and select sequences by criteria (length, ID, GC content, N content, motifs, patterns, description) using Biop…

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bio-flow-cytometry-bead-normalization Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-elemen…

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bio-flow-cytometry-clustering-phenotyping Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSO…

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bio-flow-cytometry-compensation-transformation Corrects fluorophore spillover (conventional compensation) or spectral overlap (spectral unmixing) and applies varian…

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bio-flow-cytometry-cytometry-qc Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowC…

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bio-flow-cytometry-differential-analysis Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell popul…

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bio-flow-cytometry-doublet-detection Detects and removes doublets/aggregates from flow, spectral, and mass cytometry before clustering or quantification. …

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bio-flow-cytometry-fcs-handling Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTO…

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bio-flow-cytometry-gating-analysis Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) …

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bio-gatk-variant-calling Call germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow. Covers the local-reas…

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bio-genome-assembly-assembly-polishing Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched too…

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bio-genome-assembly-assembly-qc Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), c…

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bio-genome-assembly-contamination-detection Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a s…

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bio-genome-assembly-hifi-assembly Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi…

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bio-genome-assembly-long-read-assembly Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph),…

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bio-genome-assembly-metagenome-assembly Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEG…

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bio-genome-assembly-scaffolding Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap sp…

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bio-genome-assembly-short-read-assembly Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT…

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bio-genome-intervals-bed-file-basics Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate t…

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bio-genome-intervals-bedgraph-handling Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with b…

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bio-genome-intervals-bigwig-tracks Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate…

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bio-genome-intervals-coverage-analysis Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (w…

smithery/gptomics

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