Bioconductor Package Maintainer

Bioconductor Package Maintainer

54 packages on Bioconductor

annotate

bioconductor
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Using R enviroments for annotation.

AnnotationDbi

bioconductor
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Provides user interface and database connection code for annotation data packages using SQLite data storage.

AnnotationForge

bioconductor
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Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

AnnotationHubData

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These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

AnnotationHubServer

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AnnotationHub Server component

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AnnotationHub Server component

Biobase

bioconductor
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Functions that are needed by many other packages or which replace R functions.

BiocCaseStudies

bioconductor
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Software and data to support the case studies.

BiocCheck

bioconductor
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Executes Bioconductor-specific package checks.

BiocCloud

bioconductor
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Convenience functions for the Bioconductor Amazon Machine Image

BiocContributions

bioconductor
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A set of tools for cleaning up, post-processing, adding packages to the repository, and for emailing people etc.

BiocGenerics

bioconductor
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S4 generic functions needed by many Bioconductor packages.

BiocInstaller

bioconductor
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This package is used to install and update Bioconductor, CRAN, and (some) github packages.

BiocParallel

bioconductor
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This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

BiocStyle

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Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

biocViews

bioconductor
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structures for vocabularies and narratives of views

bioDist

bioconductor
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A collection of software tools for calculating distance measures.

Category

bioconductor
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A collection of tools for performing category analysis.

chipseq

bioconductor
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Tools for helping process short read data for chipseq experiments

CoCiteStats

bioconductor
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A collection of software tools for dealing with co-citation data.

codetoolsBioC

bioconductor
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Bioconductor extensions for R code analysis tools.

DynDoc

bioconductor
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A set of functions to create and interact with dynamic documents and vignettes.

ensemblVEP

bioconductor
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Query the Ensembl Variant Effect Predictor via the perl API

ExperimentHub

bioconductor
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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.

ExperimentHubData

bioconductor
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Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.

genefilter

bioconductor
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Some basic functions for filtering genes

GeneMeta

bioconductor
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A collection of meta-analysis tools for analysing high throughput experimental data

geneplotter

bioconductor
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Functions for plotting genomic data

GenomeInfoDb

bioconductor
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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.

GenomicAlignments

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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.

GenomicFeatures

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A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

GenomicFiles

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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.

GenomicRanges

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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.

GOstats

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A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

gpls

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Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.

graph

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A package that implements some simple graph handling capabilities.

GSEABase

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This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

hypergraph

bioconductor
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A package that implements some simple capabilities for representing and manipulating hypergraphs.

Icens

bioconductor
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Many functions for computing the NPMLE for censored and truncated data.

IRanges

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The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible.

KEGGREST

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A package that provides a client interface to the KEGG REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.

OrganismDbi

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The 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.

ppiStats

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Tools for the analysis of protein interaction data.

RBGL

bioconductor
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A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

RGalaxy

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Given an R function and its manual page, make the documented function available in Galaxy.

Rhtslib

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This package provides version 1.1 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").

RNAseq

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Tools for helping process short read data from RNAseq experiments

Rsamtools

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This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

S4Vectors

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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, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

ShortRead

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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.

SummarizedExperiment

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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.

UniProt.ws

bioconductor
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A collection of functions for retrieving, processing and repackaging the UniProt web services.

VariantAnnotation

bioconductor
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Annotate variants, compute amino acid coding changes, predict coding outcomes.

zlibbioc

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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.