GenomicRanges - 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
geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-packagegenomicranges
18.56 score 47 stars 1.8k dependents 31k scripts 124k downloadsBiostrings - 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
sequencematchingalignmentsequencinggeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package
18.34 score 70 stars 1.5k dependents 14k scripts 122k 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
infrastructuredatarepresentationbioconductor-packagecore-package
17.16 score 18 stars 2.4k dependents 2.4k scripts 185k 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
geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package
17.11 score 39 stars 1.4k dependents 14k scripts 120k 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
infrastructuredatarepresentationbioconductor-packagecore-packageopenmp
16.68 score 24 stars 2.1k dependents 3.7k scripts 148k downloadsBiocManager - Access the Bioconductor Project Package Repository
The Bioconductor project publishes packages on a six-month release cycle. This package is a convenient tool to install and update Bioconductor packages. For more information about Bioconductor, see <https://bioconductor.org>.
Last updated
core-services
16.60 score 77 stars 611 dependents 4.4k scripts 310k 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
infrastructuredatarepresentationannotationgenomeannotationbioconductor-packagecore-packageu24ca289073
16.01 score 29 stars 1.3k dependents 996 scripts 132k 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
geneticsdatarepresentationannotationgenomeannotationbioconductor-packagecore-package
15.82 score 37 stars 380 dependents 3.1k scripts 93k 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
dataimportsequencingcoveragealignmentqualitycontrolbioconductor-packagecore-packagecurlbzip2xz-utilszlibcpp
15.80 score 31 stars 682 dependents 5.6k scripts 67k downloadsAnnotationDbi - Manipulation of SQLite-based annotations in Bioconductor
Implements a user-friendly interface for querying SQLite-based annotation data packages.
Last updated
annotationmicroarraysequencinggenomeannotationbioconductor-packagecore-package
15.71 score 10 stars 811 dependents 6.3k scripts 94k 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
annotationpathwaysthirdpartyclientkeggbioconductor-packagecore-package
15.51 score 15 stars 998 dependents 1.7k scripts 94k 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
geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package
15.37 score 26 stars 372 dependents 6.5k scripts 41k downloadsBiocGenerics - S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Last updated
infrastructurebioconductor-packagecore-package
15.22 score 13 stars 2.9k dependents 1.3k scripts 159k 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
infrastructurebioconductor-packagecore-packageu24ca289073cpp
15.08 score 69 stars 1.2k dependents 45 scripts 129k downloadsBSgenome - Software infrastructure for efficient representation of full genomes and their SNPs
Infrastructure shared by all the Biostrings-based genome data packages.
Last updated
geneticsinfrastructuredatarepresentationsequencematchingannotationsnpbioconductor-packagecore-package
14.53 score 10 stars 279 dependents 2.2k scripts 30k 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
infrastructuredataimportgeneticssequencingrnaseqsnpcoveragealignmentimmunooncologybioconductor-packagecore-package
14.40 score 12 stars 637 dependents 4.1k scripts 58k downloadsBiobase - Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R functions.
Last updated
infrastructurebioconductor-packagecore-package
14.18 score 9 stars 2.0k dependents 34 scripts 126k 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
infrastructuredatarepresentationdataimportsequencingrnaseqcoverageannotationgenomeannotationsinglecellimmunooncologybioconductor-packagecore-packageu24ca289073
13.42 score 12 stars 164 dependents 1.7k scripts 42k 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
infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
13.17 score 11 stars 204 dependents 1.6k scripts 17k 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
infrastructuredatarepresentationbioconductor-packagecore-packageu24ca289073openmp
13.12 score 13 stars 1.4k dependents 126 scripts 125k 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
dataimportcore-packageu24ca289073
13.02 score 14 stars 541 dependents 788 scripts 55k 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
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
12.43 score 8 stars 57 dependents 2.2k scripts 13k 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
infrastructuresoftwarebioconductor-packagecore-package
11.86 score 12 stars 1.5k dependents 312 scripts 105k 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
infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
11.73 score 20 stars 132 dependents 13 scripts 33k downloadsGenomicDataCommons - NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
Last updated
dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette
11.67 score 90 stars 14 dependents 265 scripts 2.2k 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
infrastructuredatarepresentationbioconductor-packagecore-packageu24ca289073
11.28 score 7 stars 1.3k dependents 21 scripts 94k 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
dataimportsequencingbioconductor-packagecore-packagecurlbzip2xz-utilszlib
11.17 score 11 stars 639 dependents 1 scripts 59k 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
infrastructuredatarepresentationbioconductor-packagecore-packagezlib
10.65 score 3 stars 1.9k dependents 2 scripts 140k 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
infrastructurebioconductor-packagecore-services
10.64 score 10 stars 8 dependents 123 scripts 5.7k 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
annotationinfrastructuresoftwarebioconductor-packagecore-package
10.58 score 5 stars 197 dependents 75 scripts 21k 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
infrastructurebioconductor-packagecore-package
10.57 score 4 stars 18 dependents 48 scripts 9.4k 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
infrastructuredataimportannotationgenomeannotationgenomeassemblygeneticssequencingbioconductor-packagecore-package
10.56 score 5 stars 67 dependents 437 scripts 8.2k downloadsAnVIL - Bioconductor on the AnVIL compute environment
The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides programatic access to the Dockstore, Leonardo, Rawls, TDR, and Terra RESTful programming interfaces. For platform-specific user-level functionality, see either the AnVILGCP or AnVILAz package.
Last updated
infrastructureu24hg010263
10.47 score 7 stars 12 dependents 347 scripts 1.2k downloadsSeqinfo - A simple S4 class for storing basic information about a collection of genomic sequences
The Seqinfo class stores the names, lengths, circularity flags, and genomes for a particular collection of sequences. These sequences are typically the chromosomes and/or scaffolds of a specific genome assembly of a given organism. Seqinfo objects are rarely used as standalone objects. Instead, they are used as part of higher-level objects to represent their seqinfo() component. Examples of such higher-level objects are GRanges, RangedSummarizedExperiment, VCF, GAlignments, etc... defined in other Bioconductor infrastructure packages.
Last updated
infrastructuredatarepresentationgenomeassemblyannotationgenomeannotationbioconductor-packagecore-package
10.43 score 1 stars 2.2k dependents 27 scripts 76k 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
annotationdataimportbioconductor-packagecore-package
10.37 score 1 stars 601 dependents 49 scripts 44k 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
annotationinfrastructurebioconductor-packagecore-package
9.81 score 5 stars 19 dependents 275 scripts 4.2k downloadsBiocBaseUtils - Utility and internal functions for Bioconductor packages
The package coalesces typical helper functions that are scattered throughout the Bioconductor ecosystem. It aims to reduce code redundancy by formalizing functions often used by Bioconductor developers. These functions include operations such as replacing slots in an object, selecting observations for show methods, labeling function life cycles, and more.
Last updated
softwareinfrastructurebioconductor-packagecore-package
9.74 score 4 stars 1.3k dependents 11 scripts 22k downloadsh5mread - A fast HDF5 reader
The main function in the h5mread package is h5mread(), which allows reading arbitrary data from an HDF5 dataset into R, similarly to what the h5read() function from the rhdf5 package does. In the case of h5mread(), the implementation has been optimized to make it as fast and memory-efficient as possible.
Last updated
infrastructuredatarepresentationdataimportu24ca289073curlopenssl
9.71 score 3 stars 205 dependents 4 scripts 23k 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
infrastructuregenomeassemblyannotationgenomeannotationdataimportbioconductor-packagecore-package
9.52 score 1 stars 372 dependents 16 scripts 47k 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
softwarebioconductor-packagecore-package
9.51 score 15 stars 41 dependents 21 scripts 16k 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
annotationinfrastructuregokeggbiocartabioconductor-packagecore-package
9.30 score 10 stars 6 dependents 275 scripts 1.6k downloadscigarillo - Efficient manipulation of CIGAR strings
CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR strings are found in the BAM files produced by most aligners and in the AIRR-formatted output produced by IgBLAST. The cigarillo package provides functions to parse and inspect CIGAR strings, trim them, turn them into ranges of positions relative to the "query space" or "reference space", and project positions or sequences from one space to the other. Note that these operations are low-level operations that the user rarely needs to perform directly. More typically, they are performed behind the scene by higher-level functionality implemented in other packages like Bioconductor packages GenomicAlignments and igblastr.
Last updated
infrastructurealignmentsequencematchingsequencingbioconductor-packagecore-package
9.17 score 637 dependents 8 scripts 31k 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
infrastructuredatarepresentationcopynumbercore-packagedata-structuremutationsu24ca289073
8.79 score 5 stars 16 dependents 108 scripts 2.0k downloadsGenomicFiles - 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.
Last updated
geneticsinfrastructuredataimportsequencingcoveragebioconductor-packagecore-packageu24ca289073
8.53 score 3 stars 18 dependents 112 scripts 1.7k 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
alignmentsequencematchingsequencinggeneticsbioconductor-package
7.84 score 1 stars 113 dependents 1 scripts 13k downloadsZarrArray - Bring Zarr datasets in R as DelayedArray objects
The ZarrArray package leverages the Rarr package to bring Zarr datasets in R as DelayedArray objects. The main class in the package is the ZarrArray class. A ZarrArray object is an array-like object that represents a Zarr dataset in R. ZarrArray objects are DelayedArray derivatives and therefore support all operations (delayed or block-processed) supported by DelayedArray objects.
Last updated
infrastructuredatarepresentationdataimportbioconductor-packagecore-packageu24ca289073
7.48 score 5 stars 8 dependents 13 scripts 800 downloadsOSCA - Orchestrating Single Cell Analysis with Bioconductor
Online book for orchestrating single cell analysis with Bioconductor. Contains plenty of worked examples, theoretical background and some philosophical discussions on the nature of single-cell data analysis.
Last updated
immunooncologyworkflowworkflowsinglecellworkflowbookbook-baserna-seqsingle-cellsingle-cell-rna-seqdatapkg
6.92 score 69 starsBSgenomeForge - 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
infrastructuredatarepresentationgenomeassemblyannotationgenomeannotationsequencingalignmentdataimportsequencematchingbioconductor-packagecore-package
6.57 score 5 stars 30 scripts 632 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
geneexpressionrnaseqdnamethylationnetworkinferencenetworkgraphandnetworkbiomedicalinformaticssystemsbiologytranscriptomicsclassificationclusteringdimensionreductionprincipalcomponentmrnamicroarraynormalizationgenepredictionkeggsurvivalcore-services
6.34 score 78 stars 1 scripts 379 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
infrastructuredatarepresentationsequencinggenotypingarray
6.33 score 5 stars 2 dependents 12 scripts 478 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
softwareinfrastructureu24hg010263
6.22 score 17 dependents 82 scripts 812 downloadsMultipleAlignment - Representation of multiple sequence alignments in Bioconductor
The package implements a set of S4 classes (DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment) for representing Multiple Sequence Alignments (MSA). The classes allow users to represent groups of aligned DNA, RNA or amino acid sequences as a single object. The package also provides functions to read/write such object from/to traditional MSA file formats including Stockholm and Clustal.
Last updated
alignmentmultiplesequencealignmentgeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package
5.95 score 15 dependents 5 scripts 630 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
geneticsannotationdatarepresentationvisualizationsequencingrnaseqgeneexpressionalternativesplicingtranscriptionimmunooncologybioconductor-package
5.89 score 3 stars 29 scripts 680 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 use the API calls from the AnVIL package. It coordinates AnVIL workspace functionality with native GCP tools.
Last updated
softwareinfrastructurethirdpartyclientdataimportu24hg010263
5.60 score 5 dependents 44 scripts 358 downloadsAnVILPublish - Publish Packages and Other Resources to AnVIL Workspaces
Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the 'DASHBOARD'. Vignettes are translated to python notebooks ready for evaluation in AnVIL.
Last updated
infrastructuresoftwareu24hg010263
5.57 score 1 dependents 2 scripts 330 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
infrastructuredatarepresentation
5.56 score 2 stars 2 dependents 5 scripts 584 downloadsGCPtools - Tools for working with gcloud and gsutil
Lower-level functionality to interface with Google Cloud Platform tools. 'gcloud' and 'gsutil' are both supported. The functionality provided centers around utilities for the AnVIL platform.
Last updated
softwareinfrastructurethirdpartyclientdataimportbioconductor-packageu24hg010263
5.47 score 15 dependents 22 scripts 700 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
dataimportinfrastructuresoftwarethirdpartyclientbioconductor-package
5.31 score 3 stars 10 scripts 1.4k 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
softwareinfrastructurethirdpartyclientu24hg010263
5.08 score 5 scripts 280 downloadsshinybiocloader - Use a Shiny Bioconductor CSS loader
Add a Bioconductor themed CSS loader to your shiny app. It is based on the shinycustomloader R package. Use a spinning Bioconductor note loader to enhance your shiny app loading screen. This package is intended for developer use.
Last updated
softwareinfrastructureguibioconductor-packagequarto
4.78 score 2 dependents 5 scripts 222 downloadsBiocAzul - Programmatic Access to the Azul API
Represents the OpenAPI v2 Azul API as an R object for performing requests. The infrastructure uses the AnVIL and rapiclient packages. Users can connect to either the AnVIL or Human Cell Atlas Data Explorers.
Last updated
softwareinfrastructuredataimportthirdpartyclientu24hg010263
4.70 score 2 scripts 241 downloadsBiocPkgDash - An interactive Shiny dashboard for Bioconductor package maintainers
This package provides an interactive Shiny dashboard for Bioconductor package maintainers. It visualizes various package statuses, metadata, and development metrics, offering insights into package health and activity. This tool aims to support maintainers of multiple packages by filtering packages via maintainer email.
Last updated
softwareinfrastructurevisualizationguiu24ca289073
4.65 score 4 scripts 258 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
infrastructuredatarepresentationsequencingannotationgenomeannotationgenotypingarray
4.60 score 1 stars 2 scripts 321 downloadsAnVILVRS - Expose the vrs_anvil_toolkit Python package via R
Process Variant Call Format (VCF) files and perform lookup operations on Genomic Variation Representation Service (GA4GH VRS) identifiers. The GA4GH VRS identifiers provide a standardized way to represent genomic variations, making it easier to exchange and share genomic information.
Last updated
softwarebiologicalquestionvariantannotationinfrastructurethirdpartyclientu24hg010263
4.54 score 2 scripts 119 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
infrastructuredatarepresentationbioconductor-packagecore-package
4.48 score 1 stars 6 scripts 372 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
softwareshinyapps
4.18 score 5 scripts 400 downloadsBioc.gff - Read and write GFF and GTF files
Parse GFF and GTF files using C++ classes. The package also provides utilities to read and write GFF3 files. The GFF (General Feature Format) format is a tab-delimited file format for describing genes and other features of DNA, RNA, and protein sequences. GFF files are often used to describe the features of genomes.
Last updated
softwareinfrastructuredataimportbioconductor-package
3.00 score 217 downloads