Source

smithery.ai

37,462 skills · 110K combined installs

Skills from this source

#

Skill

Source

8W Activity

Installs

bio-metagenomics-visualization Turns a shotgun profiler table (MetaPhlAn relative abundance, Bracken counts, HUMAnN function tables) into honest fig…

bio-methylation-bismark-alignment Aligns bisulfite-converted (WGBS, RRBS, PBAT) and enzymatic (EM-seq) short reads to an in-silico C->T/G->A-converted …

bio-methylation-calling Extracts per-cytosine methylation calls from aligned bisulfite/EM-seq reads with bismark_methylation_extractor (Bisma…

bio-methylation-dmr-detection Detects differentially methylated regions (DMRs) from short-read bisulfite (WGBS/RRBS), array, and long-read methylat…

bio-methylation-methylkit Imports Bismark coverage or cytosine-report files into the methylKit object model, then runs the import-to-results sp…

bio-microbiome-amplicon-processing Infers exact amplicon sequence variants (ASVs) from demultiplexed 16S rRNA or ITS amplicon FASTQ with DADA2 - removin…

bio-microbiome-differential-abundance Tests which individual taxa differ between groups on an amplicon ASV/feature table (phyloseq) using compositionally-a…

bio-microbiome-diversity-analysis Alpha and beta diversity of an amplicon (16S/ITS) ASV/OTU community table - observed features, Shannon, Pielou evenne…

bio-microbiome-functional-prediction Predicts community functional POTENTIAL from 16S/ITS amplicon ASVs with PICRUSt2 (or q2-picrust2) by phylogenetic int…

bio-microbiome-qiime2-workflow Operates the QIIME2 framework as the glue for an amplicon analysis - the .qza/.qzv artifact model, semantic types (Fe…

bio-microbiome-taxonomy-assignment Assigns taxonomy to amplicon ASVs/OTUs (16S, ITS, 18S) with a classifier conditioned on a reference database and prim…

bio-motif-search Find sequence motifs, degenerate IUPAC patterns, and transcription-factor binding sites in DNA/RNA using Biopython an…

bio-multi-omics-mixomics-analysis Builds supervised and unsupervised multivariate integration across bulk omics blocks with mixOmics - sPLS for sparse …

bio-multi-omics-mofa-integration Discovers shared and view-specific latent factors across bulk multi-omics blocks (RNA-seq, proteomics, methylation) o…

bio-multi-omics-similarity-network Stratifies patients into multi-omics subtypes by building one patient-by-patient similarity network per omic, fusing …

bio-paired-end-fastq Handle paired-end FASTQ files (R1/R2) using Biopython while keeping mates synchronized. Use when working with Illumin…

bio-pathway-go-enrichment Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hyp…

bio-pathway-gsea Tests a ranked gene vector for coordinated expression shifts in GO, KEGG, Reactome, or MSigDB gene sets with clusterP…

bio-pathway-reactome Tests a gene list or ranked gene vector for over-representation or coordinated shifts in Reactome's curated, peer-rev…

bio-pathway-wikipathways Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pa…

bio-phasing-imputation-genotype-imputation Imputes untyped genotypes against a phased reference panel with Beagle, Minimac4, or IMPUTE5 (array data) or from gen…

bio-phasing-imputation-haplotype-phasing Estimates haplotype phase from population linkage disequilibrium with SHAPEIT5, SHAPEIT4, Eagle2, or Beagle - turning…

bio-phasing-imputation-imputation-qc Assesses and filters phasing/imputation output - the quality metrics (Beagle DR2, Minimac R2 and EmpRsq, IMPUTE/GLIMP…

bio-phasing-imputation-reference-panels Selects and prepares the reference panel that phasing/imputation copies haplotypes from (1000 Genomes, HRC, TOPMed, H…

bio-phylo-distance-calculations Build model-corrected evolutionary distance matrices and distance trees (NJ, BIONJ, FastME, UPGMA) with Biopython Bio…

bio-phylo-modern-tree-inference Infers maximum-likelihood phylogenetic trees with IQ-TREE2 and RAxML-NG -- model selection (ModelFinder), branch supp…

bio-phylo-tree-io Read, write, and convert phylogenetic tree files with Biopython Bio.Phylo, and choose an annotation-preserving parser…

bio-phylo-tree-manipulation Edit phylogenetic tree structure with Biopython Bio.Phylo, and treat rooting as a separate statistical inference rath…

bio-phylo-tree-visualization Draw and export phylogenetic trees with Bio.Phylo plus matplotlib, and route rich figures to ggtree, ETE4, or iTOL. C…

bio-pileup-generation Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant callin…

bio-population-genetics-association-testing Single-variant common-variant GWAS with plink2 --glm (linear/logistic, Firth) and the linear mixed models GEMMA, BOLT…

bio-population-genetics-linkage-disequilibrium Computes linkage disequilibrium (r2, D', composite Rogers-Huff r2), prunes correlated variants, clumps GWAS summary s…

bio-population-genetics-plink-basics Manages PLINK genotype filesets - format conversion (VCF, BED/BIM/FAM, PED/MAP, pgen/pvar/psam) and sample/variant QC…

bio-population-genetics-population-structure Infers and describes population structure with PCA (plink2 --pca, smartpca/EIGENSOFT, FlashPCA2), model-based cluster…

bio-population-genetics-scikit-allel-analysis In-memory Python population genetics with scikit-allel - GenotypeArray/HaplotypeArray/AlleleCountsArray, diversity (p…

bio-primer-design-primer-basics Designs and ranks PCR primer pairs for a target template with primer3-py (design_primers), returning pairs with neare…

bio-primer-design-primer-validation Validates chosen PCR/qPCR oligos for intramolecular thermodynamic liabilities with primer3-py - hairpins, self-dimers…

bio-primer-design-qpcr-primers Co-designs qPCR/RT-qPCR primers and hydrolysis (TaqMan) or molecular-beacon probes with primer3-py (PRIMER_PICK_INTER…

bio-proteomics-data-import Loads mass-spectrometry data into Python/R and strips the search engine's bookkeeping before any number is trusted --…

bio-proteomics-differential-abundance Tests for differentially abundant proteins between conditions with limma/DEqMS empirical-Bayes moderation, proDA/msqr…

bio-proteomics-protein-inference Groups proteins from peptide identifications and controls protein-level FDR, framing inference as a chosen explanatio…

bio-proteomics-proteomics-qc Quality control for bottom-up proteomics across three levels -- instrument/raw-signal (mass accuracy, RT/iRT fit, FWH…

bio-proteomics-quantification Quantifies protein abundance from mass spectrometry using label-free (LFQ/MaxLFQ, DIA fragment-level), isobaric (TMT/…

bio-proteomics-spectral-libraries Builds and manages DIA spectral libraries as peptide query parameters (precursor m/z, a few fragment m/z plus relativ…

bio-read-alignment-bowtie2-alignment Aligns DNA short reads to a reference with Bowtie2, choosing end-to-end (whole read must align) vs local (soft-clip r…

bio-read-alignment-bwa-alignment Aligns DNA short reads (paired- or single-end) to a reference genome with bwa-mem2, the maintained successor to BWA-M…

bio-read-alignment-hisat2-alignment Aligns RNA-seq reads to a genome with HISAT2, the splice-aware aligner whose hierarchical graph FM-index runs at roug…

bio-read-alignment-star-alignment Aligns RNA-seq reads to a genome with STAR, the fast splice-aware aligner whose splice-junction database (built from …

bio-read-qc-adapter-trimming Removes sequencing adapters from FASTQ reads with Cutadapt and Trimmomatic, including paired-end read-through, small-…

bio-read-qc-contamination-screening Detects contamination in sequencing reads - cross-species (FastQ Screen, Kraken2), vector/PhiX/adapter, rRNA, and sam…