Source

smithery.ai

37,462 skills · 110K combined installs

Skills from this source

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Skill

Source

8W Activity

Installs

bio-read-qc-fastp-workflow Runs all-in-one FASTQ preprocessing with fastp in a single pass - adapter trimming via paired-end overlap analysis, q…

bio-read-qc-quality-reports Generates and interprets per-file and cross-sample QC reports from FASTQ data with FastQC, falco, and MultiQC, coveri…

bio-read-qc-umi-processing Extracts UMIs and collapses reads to original molecules with umi_tools (directional dedup) or builds error-corrected …

bio-read-sequences Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between str…

bio-reference-operations Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, …

bio-reporting-automated-qc-reports Aggregates per-tool QC metrics (FastQC, fastp, alignment, quantification, variant calling, single-cell) into one inte…

bio-reporting-figure-export Exports publication-ready figures with the correct vector/raster split, embedded editable fonts, color-space-robust p…

bio-reporting-quarto-reports Builds reproducible Quarto reports, presentations, and websites across R, Python, and Julia, with correct engine sele…

bio-reporting-rmarkdown-reports Creates reproducible R Markdown analysis reports (HTML, PDF, Word) with knitr, covering the render pipeline, the inte…

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

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

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

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

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

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

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

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

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

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

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

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

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

bio-sam-bam-basics Install the bio-sam-bam-basics skill for your AI agent. Published on smithery.ai.

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

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

bio-sequence-similarity Install the bio-sequence-similarity skill for your AI agent. Published on smithery.ai.

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

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

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

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

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

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…

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

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

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

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

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

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 …

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…

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

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

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

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

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

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

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

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

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

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

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