DelayedMatrixStats - Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.
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infrastructuredatarepresentationsoftware
11.88 score 15 stars 167 dependents 564 scripts 35k downloadsMatrixGenerics - S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.
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infrastructuresoftwarebioconductor-packagecore-package
11.70 score 12 stars 1.4k dependents 251 scripts 100k downloadsOSCA.basic - Single-Cell Analysis Basics
Most of the content in this book has been migrated to scrapbook (https://bioconductor.org/books/release/scrapbook). This book is only retained to provide redirections to the relevant scrapbook chapters.
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immunooncologyworkflowworkflowsinglecellworkflowdatapkg
6.66 score 17 stars 1 dependentsGenomicTuples - Representation and Manipulation of Genomic Tuples
GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.
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infrastructuredatarepresentationsequencingcpp
5.40 score 5 stars 7 scripts 610 downloadsOSCA.workflows - OSCA Workflows
Deploys the workflows of the "Orchestrating Single Cell Analysis with Bioconductor" book. This contains worked case studies of analyses of a variety of single-cell datasets, each proceeding from a SingleCellExperiment object. Exposition is generally minimal other than for dataset-specific justifications for parameter tweaks; refer to the other books in the OCSA collection for a detailed explanation of the theoretical basis of each step. It is intended for readers who already know the background and just want some code to copy and paste into their own analyses.
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immunooncologyworkflowworkflowsinglecellworkflowdatapkg
4.95 score 4 stars 1 dependentsMethylSeqData - Collection of Public DNA Methylation Sequencing Datasets
Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata.
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experimenthubexperimentdatasequencingdatahomo_sapiens_datamus_musculus_datamethylseqdatadatapkg
3.30 score 2 scripts