Biostrings - Efficient manipulation of biological strings
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Last updated 19 days ago
sequencematchingalignmentsequencinggeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package
17.83 score 61 stars 1.2k dependents 8.6k scripts 96k downloadsGenomicRanges - Representation and manipulation of genomic intervals
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.
Last updated 4 months ago
geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package
17.75 score 44 stars 1.3k dependents 13k scripts 87k downloadsBiocParallel - Bioconductor facilities for parallel evaluation
This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.
Last updated 21 days ago
infrastructurebioconductor-packagecore-packageu24ca289073cpp
17.40 score 67 stars 1.1k dependents 7.3k scripts 79k downloadsSummarizedExperiment - 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.
Last updated 4 months ago
geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package
16.85 score 34 stars 1.2k dependents 8.6k scripts 82k downloadsGenomeInfoDb - Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
Last updated 2 months ago
geneticsdatarepresentationannotationgenomeannotationbioconductor-packagecore-package
16.46 score 32 stars 1.7k dependents 1.3k scripts 108k downloadsBiobase - Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R functions.
Last updated 4 months ago
infrastructurebioconductor-packagecore-package
16.45 score 9 stars 1.8k dependents 6.6k scripts 93k downloadsBiocManager - Access the Bioconductor Project Package Repository
A convenient tool to install and update Bioconductor packages.
Last updated 26 days ago
core-services
16.40 score 74 stars 413 dependents 2.9k scripts 215k downloadsS4Vectors - Foundation of vector-like and list-like containers in Bioconductor
The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
Last updated 29 days ago
infrastructuredatarepresentationbioconductor-packagecore-package
16.10 score 18 stars 1.8k dependents 1.0k scripts 110k downloadsIRanges - Foundation of integer range manipulation in Bioconductor
Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
Last updated 28 days ago
infrastructuredatarepresentationbioconductor-packagecore-package
16.09 score 22 stars 1.8k dependents 2.1k scripts 105k downloadsDelayedArray - 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.
Last updated 26 days ago
infrastructuredatarepresentationannotationgenomeannotationbioconductor-packagecore-packageu24ca289073
15.66 score 26 stars 1.2k dependents 538 scripts 88k downloadsRsamtools - Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
This 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.
Last updated 4 months ago
dataimportsequencingcoveragealignmentqualitycontrolbioconductor-packagecore-packagecurlbzip2xz-utilszlibcpp
15.42 score 28 stars 566 dependents 3.2k scripts 47k downloadsGenomicAlignments - Representation and manipulation of short genomic alignments
Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
Last updated 4 months ago
infrastructuredataimportgeneticssequencingrnaseqsnpcoveragealignmentimmunooncologybioconductor-packagecore-package
15.34 score 10 stars 524 dependents 3.1k scripts 43k downloadsGenomicFeatures - Query the gene models of a given organism/assembly
Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.
Last updated 4 months ago
geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package
15.34 score 26 stars 339 dependents 5.3k scripts 34k downloadsAnnotationDbi - Manipulation of SQLite-based annotations in Bioconductor
Implements a user-friendly interface for querying SQLite-based annotation data packages.
Last updated 4 months ago
annotationmicroarraysequencinggenomeannotationbioconductor-packagecore-package
15.05 score 9 stars 769 dependents 3.6k scripts 67k downloadsKEGGREST - Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
A 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 is based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.
Last updated 4 months ago
annotationpathwaysthirdpartyclientkeggbioconductor-packagecore-package
14.46 score 9 stars 775 dependents 688 scripts 66k downloadsBiocGenerics - S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Last updated 1 months ago
infrastructurebioconductor-packagecore-package
14.22 score 12 stars 2.2k dependents 612 scripts 105k downloadsBSgenome - Software infrastructure for efficient representation of full genomes and their SNPs
Infrastructure shared by all the Biostrings-based genome data packages.
Last updated 2 months ago
geneticsinfrastructuredatarepresentationsequencematchingannotationsnpbioconductor-packagecore-package
14.12 score 9 stars 269 dependents 1.2k scripts 25k downloadsAnnotationHub - Client to access AnnotationHub resources
This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.
Last updated 4 months ago
infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
13.89 score 17 stars 102 dependents 2.7k scripts 18k downloadsBiocFileCache - Manage Files Across Sessions
This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.
Last updated 2 months ago
dataimportcore-packageu24ca289073
13.76 score 13 stars 429 dependents 486 scripts 43k downloadsHDF5Array - HDF5 datasets as array-like objects in R
The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.
Last updated 21 days ago
infrastructuredatarepresentationdataimportsequencingrnaseqcoverageannotationgenomeannotationsinglecellimmunooncologybioconductor-packagecore-packageu24ca289073
13.19 score 12 stars 123 dependents 844 scripts 27k downloadsSparseArray - 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.
Last updated 19 days ago
infrastructuredatarepresentationbioconductor-packagecore-packageopenmp
12.68 score 8 stars 1.2k dependents 79 scripts 75k downloadsShortRead - FASTQ input and manipulation
This 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, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Last updated 4 months ago
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
12.11 score 8 stars 50 dependents 1.8k scripts 11k downloadsExperimentHub - Client to access ExperimentHub resources
This 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 metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.
Last updated 4 months ago
infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
11.98 score 9 stars 55 dependents 764 scripts 11k downloadsGenomicDataCommons - NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
Last updated 1 months ago
dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette
11.94 score 87 stars 12 dependents 238 scripts 1.8k 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.
Last updated 2 months ago
infrastructuresoftwarebioconductor-packagecore-package
11.64 score 12 stars 1.3k dependents 129 scripts 74k downloadsXVector - Foundation of external vector representation and manipulation in Bioconductor
Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).
Last updated 2 months ago
infrastructuredatarepresentationbioconductor-packagecore-packagezlib
11.36 score 2 stars 1.7k dependents 67 scripts 92k downloadsBiocStyle - Standard styles for vignettes and other Bioconductor documents
Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.
Last updated 4 months ago
softwarebioconductor-packagecore-package
11.33 score 12 stars 47 dependents 1.2k scripts 10k downloadsRhtslib - HTSlib high-throughput sequencing library as an R package
This package provides version 1.18 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").
Last updated 7 days ago
dataimportsequencingbioconductor-packagecore-packagecurlbzip2xz-utilszlib
11.25 score 11 stars 591 dependents 3 scripts 46k downloadsS4Arrays - Foundation of array-like containers in Bioconductor
The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).
Last updated 1 months ago
infrastructuredatarepresentationbioconductor-packagecore-package
10.99 score 5 stars 1.2k dependents 8 scripts 70k downloadsAnnotationFilter - Facilities for Filtering Bioconductor Annotation Resources
This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.
Last updated 4 months ago
annotationinfrastructuresoftwarebioconductor-packagecore-package
10.20 score 5 stars 162 dependents 45 scripts 18k downloadsBiocIO - Standard Input and Output for Bioconductor Packages
The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.
Last updated 4 months ago
annotationdataimportbioconductor-packagecore-package
10.20 score 1 stars 487 dependents 19 scripts 32k downloadszlibbioc - An R packaged zlib-1.2.5
This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use.
Last updated 4 months ago
infrastructurebioconductor-packagecore-package
10.12 score 68 dependents 17 scripts 108k downloadsUCSC.utils - Low-level utilities to retrieve data from the UCSC Genome Browser
A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.
Last updated 2 months ago
infrastructuregenomeassemblyannotationgenomeannotationdataimportbioconductor-packagecore-package
10.09 score 1 stars 1.7k dependents 4 scripts 54k downloadsBiocCheck - Bioconductor-specific package checks
BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.
Last updated 19 days ago
infrastructurebioconductor-packagecore-services
10.07 score 8 stars 6 dependents 114 scripts 3.7k downloadsbiocViews - Categorized views of R package repositories
Infrastructure 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 'experiment data' packages.
Last updated 4 months ago
infrastructurebioconductor-packagecore-package
9.71 score 4 stars 14 dependents 30 scripts 7.1k downloadstxdbmaker - Tools for making TxDb objects from genomic annotations
A 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 to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.
Last updated 4 months ago
infrastructuredataimportannotationgenomeannotationgenomeassemblygeneticssequencingbioconductor-packagecore-package
9.70 score 3 stars 86 dependents 92 scripts 5.2k downloadsAnnotationForge - Tools for building SQLite-based annotation data packages
Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.
Last updated 4 months ago
annotationinfrastructurebioconductor-packagecore-package
9.52 score 5 stars 19 dependents 143 scripts 3.1k downloadsRaggedExperiment - 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.
Last updated 4 months ago
infrastructuredatarepresentationcopynumbercore-packagedata-structuremutationsu24ca289073
8.96 score 4 stars 15 dependents 76 scripts 1.4k downloadsBiocBaseUtils - General utility functions for developing Bioconductor packages
The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.
Last updated 4 months ago
softwareinfrastructurebioconductor-packagecore-package
8.78 score 4 stars 158 dependents 3 scripts 11k downloadspwalign - Perform pairwise sequence alignments
The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.
Last updated 2 months ago
alignmentsequencematchingsequencinggeneticsbioconductor-package
8.42 score 1 stars 105 dependents 27 scripts 7.8k downloadsUniProt.ws - R Interface to UniProt Web Services
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. This package provides a collection of functions for retrieving, processing, and re-packaging UniProt web services. The package makes use of UniProt's modernized REST API and allows mapping of identifiers accross different databases.
Last updated 2 months ago
annotationinfrastructuregokeggbiocartabioconductor-packagecore-package
8.38 score 4 stars 4 dependents 167 scripts 714 downloadsOrganism.dplyr - dplyr-based Access to Bioconductor Annotation Resources
This package provides an alternative interface to Bioconductor 'annotation' resources, in particular the gene identifier mapping functionality of the 'org' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the 'TxDb' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).
Last updated 4 months ago
annotationsequencinggenomeannotationbioconductor-packagecore-package
6.77 score 3 stars 1 dependents 63 scripts 767 downloadsGDSArray - Representing GDS files as array-like objects
GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed.
Last updated 29 days ago
infrastructuredatarepresentationsequencinggenotypingarray
6.72 score 5 stars 2 dependents 8 scripts 498 downloadsAnVILBase - Generic functions for interacting with the AnVIL ecosystem
Provides generic functions for interacting with the AnVIL ecosystem. Packages that use either GCP or Azure in AnVIL are built on top of AnVILBase. Extension packages will provide methods for interacting with other cloud providers.
Last updated 4 months ago
softwareinfrastructure
6.68 score 19 dependents 70 scripts 233 downloadsiNETgrate - Integrates DNA methylation data with gene expression in a single gene network
The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.
Last updated 4 months ago
geneexpressionrnaseqdnamethylationnetworkinferencenetworkgraphandnetworkbiomedicalinformaticssystemsbiologytranscriptomicsclassificationclusteringdimensionreductionprincipalcomponentmrnamicroarraynormalizationgenepredictionkeggsurvivalcore-services
6.21 score 74 stars 1 scripts 170 downloadsAnVILGCP - The GCP R Client for the AnVIL
The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to work with the AnVIL package. User-level interaction with this package should be minimal.
Last updated 2 months ago
softwareinfrastructurethirdpartyclientdataimport
5.66 score 3 dependents 27 scripts 124 downloadsAnVILAz - R / Bioconductor Support for the AnVIL Azure Platform
The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVILAz package supports end-users and developers using the AnVIL platform in the Azure cloud. The package provides a programmatic interface to AnVIL resources, including workspaces, notebooks, tables, and workflows. The package also provides utilities for managing resources, including copying files to and from Azure Blob Storage, and creating shared access signatures (SAS) for secure access to Azure resources.
Last updated 4 months ago
softwareinfrastructurethirdpartyclient
5.45 score 5 scripts 120 downloadsDelayedDataFrame - Delayed operation on DataFrame using standard DataFrame metaphor
Based on the standard DataFrame metaphor, we are trying to implement the feature of delayed operation on the DelayedDataFrame, with a slot of lazyIndex, which saves the mapping indexes for each column of DelayedDataFrame. Methods like show, validity check, [/[[ subsetting, rbind/cbind are implemented for DelayedDataFrame to be operated around lazyIndex. The listData slot stays untouched until a realization call e.g., DataFrame constructor OR as.list() is invoked.
Last updated 4 months ago
infrastructuredatarepresentation
5.26 score 2 stars 1 dependents 3 scripts 270 downloadsSplicingGraphs - Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.
Last updated 4 months ago
geneticsannotationdatarepresentationvisualizationsequencingrnaseqgeneexpressionalternativesplicingtranscriptionimmunooncologybioconductor-package
5.26 score 2 stars 8 scripts 292 downloadsHubPub - Utilities to create and use Bioconductor Hubs
HubPub provides users with functionality to help with the Bioconductor Hub structures. The package provides the ability to create a skeleton of a Hub style package that the user can then populate with the necessary information. There are also functions to help add resources to the Hub package metadata files as well as publish data to the Bioconductor S3 bucket.
Last updated 2 months ago
dataimportinfrastructuresoftwarethirdpartyclientbioconductor-package
5.08 score 3 stars 4 scripts 292 downloadsVariantExperiment - A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor.
Last updated 4 months ago
infrastructuredatarepresentationsequencingannotationgenomeannotationgenotypingarray
5.00 score 1 stars 2 scripts 219 downloadsBSgenomeForge - Forge your own BSgenome data package
A set of tools to forge BSgenome data packages. Supersedes the old seed-based tools from the BSgenome software package. This package allows the user to create a BSgenome data package in one function call, simplifying the old seed-based process.
Last updated 4 months ago
infrastructuredatarepresentationgenomeassemblyannotationgenomeannotationsequencingalignmentdataimportsequencematchingbioconductor-packagecore-package
4.90 score 4 stars 6 scripts 296 downloadsSQLDataFrame - Representation of SQL tables in DataFrame metaphor
Implements bindings for SQL tables that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows SQL-derived data to be easily used inside other Bioconductor objects (e.g., SummarizedExperiments) while keeping everything on disk.
Last updated 4 months ago
datarepresentationinfrastructuresoftware
4.51 score 2 stars 5 scripts 182 downloadsupdateObject - Find/fix old serialized S4 instances
A set of tools built around updateObject() to work with old serialized S4 instances. The package is primarily useful to package maintainers who want to update the serialized S4 instances included in their package. This is still work-in-progress.
Last updated 4 months ago
infrastructuredatarepresentationbioconductor-packagecore-package
4.48 score 1 stars 3 scripts 161 downloadsBiocHubsShiny - View AnnotationHub and ExperimentHub Resources Interactively
A package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package.
Last updated 7 days ago
softwareshinyapps
3.90 score 1 scripts 182 downloads