Showing 16 of total 16 results (show query)
henrikbengtsson
matrixStats:Functions that Apply to Rows and Columns of Matrices (and to Vectors)
High-performing functions operating on rows and columns of matrices, 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. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Maintained by Henrik Bengtsson. Last updated 3 months ago.
208 stars 18.09 score 20k scripts 2.3k dependents
bioc
SummarizedExperiment:A container (S4 class) for matrix-like assays
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Maintained by Hervé Pagès. Last updated 5 months ago.
geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package
34 stars 16.84 score 8.6k scripts 1.2k dependentsbioc
DelayedArray:A unified framework for working transparently with on-disk and in-memory array-like datasets
Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.
Maintained by Hervé Pagès. Last updated 1 months ago.
infrastructuredatarepresentationannotationgenomeannotationbioconductor-packagecore-packageu24ca289073
27 stars 15.59 score 538 scripts 1.2k dependentsbioc
SparseArray:High-performance sparse data representation and manipulation in R
The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.
Maintained by Hervé Pagès. Last updated 11 days ago.
infrastructuredatarepresentationbioconductor-packagecore-packageopenmp
9 stars 12.47 score 79 scripts 1.2k dependentsbioc
SeqArray:Data management of large-scale whole-genome sequence variant calls using GDS files
Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.
Maintained by Xiuwen Zheng. Last updated 7 days ago.
infrastructuredatarepresentationsequencinggeneticsbioinformaticsgds-formatsnpsnvweswgscpp
45 stars 12.11 score 1.1k scripts 9 dependentsbioc
sparseMatrixStats:Summary Statistics for Rows and Columns of Sparse Matrices
High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.
Maintained by Constantin Ahlmann-Eltze. Last updated 5 months ago.
infrastructuresoftwaredatarepresentationcpp
54 stars 11.98 score 174 scripts 130 dependentsbioc
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.
Maintained by Peter Hickey. Last updated 3 months ago.
infrastructuredatarepresentationsoftware
16 stars 11.86 score 211 scripts 112 dependentsbioc
MatrixGenerics: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.
Maintained by Peter Hickey. Last updated 3 months ago.
infrastructuresoftwarebioconductor-packagecore-package
12 stars 11.64 score 129 scripts 1.3k dependentsbioc
RaggedExperiment:Representation of Sparse Experiments and Assays Across Samples
This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.
Maintained by Marcel Ramos. Last updated 4 months ago.
infrastructuredatarepresentationcopynumbercore-packagedata-structuremutationsu24ca289073
4 stars 8.93 score 76 scripts 14 dependentsbioc
GenomicFiles:Distributed computing by file or by range
This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
geneticsinfrastructuredataimportsequencingcoverage
6.86 score 89 scripts 16 dependents
spkaluzny
splus2R:Supplemental S-PLUS Functionality in R
Currently there are many functions in S-PLUS that are missing in R. To facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R.
Maintained by Stephen Kaluzny. Last updated 1 years ago.
1 stars 6.56 score 82 scripts 30 dependentsbioc
MultiDataSet:Implementation of MultiDataSet and ResultSet
Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.
Maintained by Xavier Escribà Montagut. Last updated 5 months ago.
6.45 score 28 scripts 10 dependentsbioc
TENxIO:Import methods for 10X Genomics files
Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.
Maintained by Marcel Ramos. Last updated 4 months ago.
softwareinfrastructuredataimportsinglecellbioconductor-packageu24ca289073
5.77 score 7 scripts 3 dependentsbioc
easyRNASeq:Count summarization and normalization for RNA-Seq data
Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.
Maintained by Nicolas Delhomme. Last updated 5 months ago.
geneexpressionrnaseqgeneticspreprocessingimmunooncology
5.43 score 15 scripts 1 dependentsbioc
SCArray:Large-scale single-cell omics data manipulation with GDS files
Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.
Maintained by Xiuwen Zheng. Last updated 5 days ago.
infrastructuredatarepresentationdataimportsinglecellrnaseqcpp
1 stars 5.32 score 9 scripts 1 dependentsbioc
VCFArray:Representing on-disk / remote VCF files as array-like objects
VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.
Maintained by Qian Liu. Last updated 5 months ago.
infrastructuredatarepresentationsequencingvariantannotation
1 stars 4.00 score 3 scripts