Source

smithery.ai

37,462 skills · 110K combined installs

Skills from this source

#

Skill

Source

8W Activity

Installs

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

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…

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

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

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),…

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

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

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…

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

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

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

bio-genome-intervals-gtf-gff-handling Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/e…

bio-genome-intervals-proximity-operations Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - near…

bio-geo-data Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when fi…

bio-hi-c-analysis-compartment-analysis Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-…

bio-hi-c-analysis-contact-pairs Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library wor…

bio-hi-c-analysis-hic-data-io Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using …

bio-hi-c-analysis-hic-differential Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompa…

bio-hi-c-analysis-hic-visualization Renders Hi-C contact matrices honestly and reproducibly with matplotlib, cooltools, HiCExplorer, pyGenomeTracks, FAN-…

bio-hi-c-analysis-matrix-operations Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected…

bio-hi-c-analysis-tad-detection Detects TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulat…

bio-imaging-mass-cytometry-cell-segmentation Segment single cells from multiplexed IMC/MIBI tissue images using Mesmer/DeepCell, Cellpose, or ilastik+CellProfiler…

bio-imaging-mass-cytometry-data-preprocessing Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover …

bio-imaging-mass-cytometry-interactive-annotation Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, coveri…

bio-imaging-mass-cytometry-phenotyping Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-…

bio-imaging-mass-cytometry-quality-metrics Quality control for IMC/MIBI data across pixel, channel, image, slide, and batch levels, covering Poisson-count SNR (…

bio-imaging-mass-cytometry-spatial-analysis Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, coveri…

bio-local-blast Build local BLAST databases and run searches using NCBI BLAST+ command-line tools.

bio-long-read-sequencing-basecalling Basecalls raw Oxford Nanopore signal (POD5/FAST5) into reads with Dorado, choosing the chemistry-matched model and ac…

bio-long-read-sequencing-clair3-variants Calls germline small variants (SNPs and indels) from Oxford Nanopore and PacBio HiFi long reads with Clair3, a two-st…

bio-long-read-sequencing-isoseq-analysis Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and …

bio-long-read-sequencing-long-read-alignment Aligns Oxford Nanopore and PacBio long reads (and assemblies) to a reference with minimap2 using the error-rate-match…

bio-long-read-sequencing-long-read-qc Assesses Oxford Nanopore and PacBio long-read quality with NanoPlot, cramino, NanoComp, pycoQC/toulligQC, and seqkit,…

bio-long-read-sequencing-medaka-polishing Polishes Oxford Nanopore draft assemblies to higher consensus accuracy with medaka, a basecaller-model-specific neura…

bio-long-read-sequencing-nanopore-methylation Calls DNA base modifications (5mC, 5hmC, 6mA, 4mC) directly from Oxford Nanopore and PacBio HiFi long reads encoded a…

bio-long-read-sequencing-structural-variants Detects structural variants (deletions, insertions, inversions, duplications, translocations) from Oxford Nanopore an…

bio-metabolomics-lipidomics Assigns honest lipid annotation levels, designs class-based internal-standard quantification, and runs lipid-aware di…

bio-metabolomics-metabolite-annotation Turns untargeted LC-MS/MS features (m/z, RT, MS/MS) into confidence-stratified metabolite annotations using spectral-…

bio-metabolomics-msdial-preprocessing Runs the MS-DIAL preprocessing workflow (peak picking, MS2Dec spectral deconvolution, alignment, gap-filling) and imp…

bio-metabolomics-normalization-qc Designs QC, corrects signal drift, removes batch effects, filters features, normalizes samples, and imputes missing v…

bio-metabolomics-pathway-mapping Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA),…

bio-metabolomics-statistical-analysis Decision-grade statistical analysis for metabolomics intensity tables. Covers transformation and scaling (Pareto vs u…

bio-metabolomics-targeted-analysis Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution…

bio-metabolomics-xcms-preprocessing Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, takin…

bio-metagenomics-abundance Turns shotgun classifier output into a defensible abundance table with Bracken Bayesian re-estimation, then compositi…

bio-metagenomics-amr-detection Profiles the antimicrobial-resistance gene content (resistome) of shotgun metagenomes - read-based quantification wit…

bio-metagenomics-functional-profiling Profiles the functional potential of shotgun metagenomes with HUMAnN 3's tiered search (MetaPhlAn prescreen, Bowtie2 …

bio-metagenomics-kraken Classifies shotgun metagenomic reads to taxa with Kraken2's minimizer/LCA matching against a chosen reference databas…

bio-metagenomics-metaphlan Profiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie…

bio-metagenomics-strain-tracking Resolves and compares bacterial strains below the species level from shotgun metagenomes with inStrain (popANI/conANI…