biomate-ai
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- ▌ Bioconductor Enhancedvolcano · biomate-aiVolcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many po
- ▌ Bioconductor Metabocoreutils · biomate-aiMetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound ma
- ▌ Bioconductor Trajectoryutils · biomate-aiImplements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime infere
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- ▌ Bioconductor Singlecellexperiment · biomate-aiDefines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metada
- ▌ Bioconductor Dirichletmultinomial · biomate-aiDirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed fu
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- ▌ Bioconductor Spatialexperiment · biomate-aiDefines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordina
- ▌ Bioconductor Variantannotation · biomate-aiAnnotate variants, compute amino acid coding changes, predict coding outcomes.
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- ▌ Bioconductor Treesummarizedexperiment · biomate-aiTreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.
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- ▌ Bioconductor Dose · biomate-aiThis package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enric
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- ▌ Bioconductor Topgo · biomate-aitopGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and
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- ▌ Bioconductor Gviz · biomate-aiGenomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to
- ▌ Bioconductor Gdsfmt · biomate-aiProvides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited
- ▌ Bioconductor Gypsum · biomate-aiClient for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the docu
- ▌ Bioconductor Qvalue · biomate-aiThis package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false
- ▌ Bioconductor Ggbio · biomate-aiThe ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor
- ▌ Bioconductor Mzr · biomate-aimzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XC
- ▌ Bioconductor Biobase · biomate-aiFunctions that are needed by many other packages or which replace R functions.
- ▌ Bioconductor Seqlogo · biomate-aiseqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).
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- ▌ Bioconductor Ggtree · biomate-ai'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.
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- ▌ Bioconductor Ebimage · biomate-aiEBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. Thi
- ▌ Bioconductor Mzid · biomate-aiA parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact th
- ▌ Bioconductor Basilisk · biomate-aiInstalls a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to e
- ▌ Bioconductor Graphite · biomate-aiGraph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.
- ▌ Bioconductor Dnacopy · biomate-aiImplements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.
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- ▌ Bioconductor Flowcore · biomate-aiProvides S4 data structures and basic functions to deal with flow cytometry data.
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- ▌ Bioconductor Annotate · biomate-aiThis tool uses the label-tree function from HyPhy to annotate a phylogenetic tree. It allows users to select a subset of leaves using either a regular expression or a list of sequence names, and then apply a specified label to these selecte
- ▌ Bioconductor Bsgenome · biomate-aiInfrastructure shared by all the Biostrings-based genome data packages.
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- ▌ Bioconductor Gosemsim · biomate-aiThe semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R packag
- ▌ Bioconductor Keggrest · biomate-aiA package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see <https://www.kegg.jp/kegg/rest/>). Note that KEGGREST
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- ▌ Bioconductor Biomart · biomate-aiIn recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. bio
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- ▌ Bioconductor Biovizbase · biomate-aiThe biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and enc
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- ▌ Bioconductor Pcamethods · biomate-aiProvides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA o
- ▌ Bioconductor Biocviews · biomate-aiInfrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and '
- ▌ Bioconductor Rsamtools · biomate-aiThis package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
- ▌ Bioconductor Shortread · biomate-aiThis package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, an
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- ▌ Bioconductor Tfbstools · biomate-aiTFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It c
- ▌ Bioconductor Txdbmaker · biomate-aiA set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and
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- ▌ Bioconductor Msnbase · biomate-aiMSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
- ▌ Bioconductor Psmatch · biomate-aiThe PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and m
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- ▌ Bioconductor Biostrings · biomate-aiMemory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
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- ▌ Bioconductor Mixomics · biomate-aiMultivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducin
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- ▌ Bioconductor Msa · biomate-aiThe 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any externa
- ▌ Bioconductor Sva · biomate-aiThe sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensi
- ▌ Bioconductor Vsn · biomate-aiThe package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of th
- ▌ Bioconductor Kegggraph · biomate-aiKEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essenti
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- ▌ Bioconductor Organismdbi · biomate-aiThe 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 these packages implements a select methods.
- ▌ Bioconductor Rtracklayer · biomate-aiExtensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/imp
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- ▌ Bioconductor Qfeatures · biomate-aiThe QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assa
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- ▌ Bioconductor Affy · biomate-aiThe package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
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- ▌ Bioconductor Gsva · biomate-aiGene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data fr
- ▌ Bioconductor Mast · biomate-aiMethods and models for handling zero-inflated single cell assay data.
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- ▌ Bioconductor Enrichplot · biomate-aiThe 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualizati
- ▌ Bioconductor Reactomepa · biomate-aiReactome is a free, open-source, curated and peer-reviewed pathway database. Their goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge.
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- ▌ Bioconductor Experimenthub · biomate-aiThis package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me
- ▌ Bioconductor Phyloseq · biomate-aiphyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.
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- ▌ Bioconductor Dada2 · biomate-aiThe dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, an
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- ▌ Bioconductor Edger · biomate-aiEstimates differential gene expression for short read sequence count using methods appropriate for count data. If you have paired data you may also want to consider Tophat/Cufflinks. Input must be raw count data for each sequence arranged i
- ▌ Bioconductor Fgsea · biomate-aiA tabular file with gene symbols in the first column, and a ranked statistic (e.g. t-statistic or log fold-change) in the second column