biomate-ai/biomate-bioconductor-kb
59 skills
$npx skills add biomate-ai/biomate-bioconductor-kbSkillInstalls
annotateThis tool uses the label-tree function from HyPhy to annotate a phylogenetic tree.basiliskInstalls a self-contained conda instance that is managed by the R/Bioconductor installation machinery.beerBEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data.biobaseFunctions that are needed by many other packages or which replace R functions.biocviewsInfrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary.biomartIn recent years a wealth of biological data has become available in public data repositories.biostringsMemory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.biovizbaseThe biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data.bsgenomeInfrastructure shared by all the Biostrings-based genome data packages.bumphunterTools for finding bumps in genomic datachipseekerChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function.clusterprofilerThis package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation.cogeqccogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable…complexheatmapComplex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns.consensusclusterplusalgorithm for determining cluster count and membership by stability evidence in unsupervised analysisdecipherA toolset for deciphering and managing biological sequences.dnacopyImplements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.doseThis package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and…doubletroubledoubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication.enrichplotThe 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis.epiallelerEpialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited.epigrahmmepigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models.experimenthubThis package provides a client for the Bioconductor ExperimentHub web resource.extrachipsThis package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data.faersThe FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs…gdsfmtProvides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files.genefilterSome basic functions for filtering genes.geneplotterFunctions for plotting genomic datagenomicalignmentsProvides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome).genomicfeaturesExtract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object.genomicrangesThe ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput…ggbioThe ggbio package extends and specializes the grammar of graphics for biological data.ggmanhManhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study.ggtree'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.gosemsimThe semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became…graphiteGraph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.gvizGenomic data analyses requires integrated visualization of known genomic information and new experimental data.gypsumClient for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem.hicdcplusSystematic 3D interaction calls and differential analysis for Hi-C and HiChIP.hicexperimentR generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats.hicontactsHiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.immunotationMHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells.kegggraphKEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs.keggrestA package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API.lintindWhen we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity…macsrThe Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites.miasimMicrobiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models.minfiTools to analyze & visualize Illumina Infinium methylation arrays.mosbiThis package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering).msa2distMSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis.multiassayexperimentHarmonize data management of multiple experimental assays performed on an overlapping set of specimens.organismdbiThe package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of…pcamethodsProvides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA.qvalueThis package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values.rblastSeamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This work was partially supported by grant no.reactomepaReactome is a free, open-source, curated and peer-reviewed pathway database.residualmatrixProvides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix.seqlogoseqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).topgotopGO package provides tools for testing GO terms while accounting for the topology of the GO graph.