smithery/gptomics

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bio-restriction-enzyme-selection Select restriction enzymes for cloning or diagnostics using Biopython Bio.Restriction.

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bio-restriction-fragment-analysis Predict restriction digest fragment sizes and gel patterns using Biopython Bio.Restriction.

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bio-restriction-sites Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction.

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bio-reverse-complement Generate reverse complements and complements of DNA/RNA sequences using Biopython, including IUPAC ambiguity codes, g…

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bio-ribo-seq-orf-detection Detect and quantify translated ORFs from Ribo-seq using 3-nucleotide periodicity, including uORFs, internal ORFs, dOR…

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bio-ribo-seq-riboseq-preprocessing Preprocess ribosome profiling reads with UMI handling, adapter trimming, contaminant/rRNA depletion, and footprint-aw…

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bio-ribo-seq-ribosome-periodicity Validate Ribo-seq library quality by measuring 3-nucleotide periodicity and calibrating read-length-specific P-site o…

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bio-ribo-seq-ribosome-stalling Detect ribosome pausing and stalling at codon resolution from Ribo-seq, using local-relative occupancy metrics and A-…

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bio-ribo-seq-translation-efficiency Quantify translation efficiency (TE) as ribosome occupancy relative to mRNA abundance and test for differential TE be…

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bio-rna-quantification-alignment-free-quant Quantify transcript expression from FASTQ with Salmon (selective alignment) or kallisto (pseudoalignment), bypassing …

smithery/gptomics

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bio-rna-quantification-count-matrix-qc Quality control and exploration of RNA-seq count matrices before differential expression.

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bio-rna-quantification-featurecounts-counting Count reads per gene from aligned BAM files using Subread featureCounts.

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bio-rna-quantification-tximport-workflow Import transcript-level quantifications from Salmon/kallisto/RSEM into R for gene-level analysis with DESeq2/edgeR us…

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bio-seq-objects Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from string…

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bio-sequence-properties Calculate nucleotide and protein sequence properties (GC content, GC skew, molecular weight, melting temperature, iso…

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bio-sequence-statistics Calculate assembly and sequence statistics (N50/L50, auN, NG50/NGA50, length distribution, GC content with ambiguity …

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bio-single-cell-batch-integration Integrate multiple scRNA-seq samples or batches with Harmony, scVI/scANVI, Seurat (CCA/RPCA), fastMNN, Scanorama, or …

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bio-single-cell-cell-annotation Automated reference-based cell type annotation for single-cell RNA-seq using CellTypist, SingleR, Azimuth, scANVI, an…

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bio-single-cell-cell-communication Infers ligand-receptor cell-cell communication from scRNA-seq with a consensus-first workflow (LIANA), plus CellPhone…

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bio-single-cell-clustering Dimensionality reduction and graph-based clustering for single-cell RNA-seq with Scanpy (Python) and Seurat (R). Reso…

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bio-single-cell-data-io Read, write, create, and convert single-cell objects across AnnData (Python), Seurat (R), and SingleCellExperiment (R…

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bio-single-cell-lineage-tracing Reconstructs single-cell lineage trees and clonal relationships from CRISPR/Cas9 scars, static expressed barcodes (LA…

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bio-single-cell-markers-annotation Detect cluster marker genes and assign manual cell type labels in single-cell RNA-seq using Scanpy (Python) and Seura…

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bio-single-cell-perturb-seq Analyze Perturb-seq / CROP-seq single-cell CRISPR screens.

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bio-single-cell-preprocessing Quality control, ambient-RNA handling, normalization, and feature selection for single-cell RNA-seq using Scanpy (Pyt…

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bio-single-cell-scatac-analysis Analyze single-cell ATAC-seq with Signac/ArchR (R) and SnapATAC2 (Python alternative).

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bio-single-cell-trajectory-inference Infers developmental trajectories, pseudotime, RNA velocity, and directed fate probabilities from single-cell data us…

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bio-small-rna-seq-differential-mirna Tests miRNAs for differential expression with DESeq2 or edgeR using small-RNA-aware normalization and filtering.

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bio-small-rna-seq-mirdeep2-analysis Discovers novel miRNAs and quantifies known miRNAs with miRDeep2 by scoring genome-mapped read stacks against the Dic…

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bio-small-rna-seq-mirge3-analysis Quantifies known miRNAs, isomiRs, tRFs, and A-to-I editing fast with miRge3.0 by aligning collapsed reads to curated …

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bio-small-rna-seq-smrna-preprocessing Trims kit-specific 3' adapters, strips UMIs or 4N degenerate ends, size-selects, and collapses small RNA-seq reads (m…

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bio-small-rna-seq-target-prediction Predicts and prioritizes miRNA target genes with seed-based tools (miRanda, TargetScan, miRDB) and experimentally val…

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bio-spatial-transcriptomics-image-analysis Segments cells/nuclei and extracts image features from imaging spatial transcriptomics (Xenium, MERFISH/MERSCOPE, Cos…

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bio-spatial-transcriptomics-spatial-communication Maps cell-cell communication and ligand-receptor co-expression in spatial transcriptomics (Visium, Xenium, MERFISH, C…

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bio-spatial-transcriptomics-spatial-data-io Loads spatial transcriptomics data from Visium, Visium HD, Xenium, MERFISH/MERSCOPE, CosMx, Slide-seq/Curio, and Ster…

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bio-spatial-transcriptomics-spatial-deconvolution Estimates per-spot cell type composition of spatial transcriptomics mixtures (Visium, Slide-seq, Stereo-seq) from an …

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bio-spatial-transcriptomics-spatial-domains Identify spatially coherent tissue domains (regions like cortical layers, tumor vs stroma) in Visium, Visium HD, Xeni…

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bio-spatial-transcriptomics-spatial-multiomics Integrates spatial RNA with a second modality (protein, ATAC, or histone marks) on spatial CITE-seq, DBiT-seq, spatia…

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bio-spatial-transcriptomics-spatial-neighbors Build the spatial neighbor graph that every downstream spatial statistic (Moran's I, neighborhood enrichment, co-occu…

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bio-spatial-transcriptomics-spatial-preprocessing Quality control, filtering, and normalization for spatial transcriptomics (Visium, Visium HD, Xenium, MERFISH/MERSCOP…

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bio-spatial-transcriptomics-spatial-proteomics Analyzes multiplexed antibody-imaging data (CODEX/PhenoCycler, MIBI-TOF, IMC, CyCIF, Opal/Vectra mIF) as continuous p…

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bio-spatial-transcriptomics-spatial-statistics Detects spatially variable genes, spatial autocorrelation, and cell-type colocalization for spatial transcriptomics u…

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bio-spatial-transcriptomics-spatial-visualization Plots spatial transcriptomics expression, clusters, and annotations on tissue using Squidpy and Scanpy. Use when choo…

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bio-sra-data Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror.…

smithery/gptomics

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bio-structural-biology-alphafold-predictions Retrieves and interprets AlphaFold Protein Structure Database (AFDB) models by UniProt accession, reading pLDDT and P…

smithery/gptomics

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bio-structural-biology-modern-structure-prediction Predicts protein and complex structures with deep-learning models (ESMFold, AlphaFold2/ColabFold, AlphaFold3, Chai-1,…

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bio-structural-biology-structure-io Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB. Use when choosing a format (…

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bio-structural-biology-structure-modification Modifies protein structures in place with Biopython Bio.PDB - transforms coordinates, strips waters/heteroatoms, over…

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bio-structural-biology-structure-navigation Navigate the Bio.PDB SMCRA hierarchy (Structure-Model-Chain-Residue-Atom) safely, surfacing the heterogeneity it hide…

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bio-tcr-bcr-analysis-immcantation-analysis Reconstructs B-cell clonal families, quantifies somatic hypermutation and selection, and builds antibody lineage tree…

smithery/gptomics

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