Rsamtools - 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.
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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.
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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.
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annotationpathwaysthirdpartyclientkeggbioconductor-packagecore-package
15.51 score 15 stars 998 dependents 1.7k scripts 94k downloadsBiobase - Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R functions.
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infrastructurebioconductor-packagecore-package
14.18 score 9 stars 2.0k dependents 34 scripts 126k 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.
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infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
13.17 score 11 stars 204 dependents 1.6k scripts 17k 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.
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dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
12.43 score 8 stars 57 dependents 2.2k scripts 13k downloadsgraph - graph: A package to handle graph data structures
A package that implements some simple graph handling capabilities.
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graphandnetwork
11.99 score 373 dependents 1.3k scripts 44k 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.
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infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
11.73 score 20 stars 132 dependents 13 scripts 33k downloadsVariantAnnotation - Annotation of Genetic Variants
Annotate variants, compute amino acid coding changes, predict coding outcomes.
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dataimportsequencingsnpannotationgeneticsvariantannotationcurlbzip2xz-utilszlib
11.69 score 164 dependents 3.1k scripts 18k downloadsannotate - Annotation for microarrays
Using R enviroments for annotation.
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annotationpathwaysgo
11.63 score 276 dependents 882 scripts 42k 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.
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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.
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infrastructurebioconductor-packagecore-package
10.57 score 4 stars 18 dependents 48 scripts 9.4k downloadsGSEABase - Gene set enrichment data structures and methods
This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
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geneexpressiongenesetenrichmentgraphandnetworkgokegg
10.43 score 83 dependents 2.6k scripts 21k downloadsRBGL - An interface to the BOOST graph library
A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.
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graphandnetworknetworkcpp
9.90 score 149 dependents 506 scripts 18k 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.
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annotationinfrastructurebioconductor-packagecore-package
9.81 score 5 stars 19 dependents 275 scripts 4.2k 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.
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softwarebioconductor-packagecore-package
9.51 score 15 stars 41 dependents 21 scripts 16k downloadsgenefilter - genefilter: methods for filtering genes from high-throughput experiments
Some basic functions for filtering genes.
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microarraycpp
8.91 score 157 dependents 3 scripts 28k downloadsgeneplotter - Graphics related functions for Bioconductor
Functions for plotting genomic data
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visualization
8.81 score 15 dependents 413 scripts 8.7k downloadsCategory - Category Analysis
A collection of tools for performing category (gene set enrichment) analysis.
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annotationgopathwaysgenesetenrichment
8.73 score 15 dependents 596 scripts 3.3k 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.
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geneticsinfrastructuredataimportsequencingcoveragebioconductor-packagecore-packageu24ca289073
8.53 score 3 stars 18 dependents 112 scripts 1.7k downloadsBiocVersion - Set the appropriate version of Bioconductor packages
This package provides repository information for the appropriate version of Bioconductor.
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infrastructure
7.78 score 268 dependents 23 scripts 162k downloadsOrganismDbi - Software to enable the smooth interfacing of different database packages
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.
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annotationinfrastructure
7.74 score 40 dependents 53 scripts 5.8k downloadsGOstats - Tools for manipulating GO and microarrays
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.
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annotationgomultiplecomparisongeneexpressionmicroarraypathwaysgenesetenrichmentgraphandnetwork
7.13 score 11 dependents 575 scripts 3.5k downloadsbioDist - Different distance measures
A collection of software tools for calculating distance measures.
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clusteringclassification
5.89 score 2 dependents 65 scripts 762 downloadsTENxBrainData - Data from the 10X 1.3 Million Brain Cell Study
Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics.
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sequencingdatarnaseqdataexpressiondatasinglecelldatadatapkg
5.43 score 1 dependents 89 scriptsAnnotationHubData - Transform public data resources into Bioconductor Data Structures
These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.
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dataimport
5.12 score 5 dependents 16 scripts 1.8k downloadschipseq - chipseq: A package for analyzing chipseq data
Tools for helping process short read data for chipseq experiments.
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chipseqsequencingcoveragequalitycontroldataimport
5.10 score 2 dependents 1.2k downloadsliftOver - Changing genomic coordinate systems with rtracklayer::liftOver
The liftOver facilities developed in conjunction with the UCSC browser track infrastructure are available for transforming data in GRanges formats. This is illustrated here with an image of the EBI/NHGRI GWAS catalog that is, as of May 10 2017, distributed with coordinates defined by NCBI build hg38.
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workflowbasicworkflow
4.85 score 357 scriptsGeneMeta - MetaAnalysis for High Throughput Experiments
A collection of meta-analysis tools for analysing high throughput experimental data
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sequencinggeneexpressionmicroarray
4.78 score 1 dependents 2 scripts 752 downloadsIcens - NPMLE for Censored and Truncated Data
Many functions for computing the NPMLE for censored and truncated data.
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infrastructure
4.46 score 7 dependents 44 scripts 1.6k downloadsgpls - Classification using generalized partial least squares
Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.
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classificationmicroarrayregression
4.32 score 17 scripts 1.2k downloadsDynDoc - Dynamic document tools
A set of functions to create and interact with dynamic documents and vignettes.
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reportwritinginfrastructure
4.18 score 6 dependents 13 scripts 3.2k downloadsarrays - Using Bioconductor for Microarray Analysis
Using Bioconductor for Microarray Analysis workflow
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workflowbasicworkflow
4.11 score 64 scriptsGSE62944 - GEO accession data GSE62944 as a SummarizedExperiment
TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub.
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experimentdatagenomednaseqdatarnaseqdatadatapkg
4.00 score 5 scriptsExperimentHubData - Add resources to ExperimentHub
Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.
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infrastructuredataimportguithirdpartyclient
3.67 score 8 scripts 1.6k downloadsLoomExperiment - LoomExperiment container
The LoomExperiment package provide a means to easily convert the Bioconductor "Experiment" classes to loom files and vice versa.
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immunooncologydatarepresentationdataimportinfrastructuresinglecell
3.26 score 89 scripts 1.0k downloadshypergraph - A package providing hypergraph data structures
A package that implements some simple capabilities for representing and manipulating hypergraphs.
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graphandnetwork
3.12 score 2 dependents 11 scripts 635 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.
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softwareinfrastructuredataimportbioconductor-package
3.00 score 217 downloadsCoCiteStats - Different test statistics based on co-citation.
A collection of software tools for dealing with co-citation data.
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software
2.60 score 5 scripts 523 downloadsvariants - Annotating Genomic Variants
Read and write VCF files. Identify structural location of variants and compute amino acid coding changes for non-synonymous variants. Use SIFT and PolyPhen database packages to predict consequence of amino acid coding changes.
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immunooncologyworkflowannotationworkflowworkflow
2.30 scorehighthroughputassays - Using Bioconductor with High Throughput Assays
The workflow illustrates use of the flow cytometry packages to load, transform and visualize the flow data and gate certain populations in the dataset. The workflow loads the `flowCore`, `flowStats` and `flowWorkspace` packages and its dependencies. It loads the ITN data with 15 samples, each of which includes, in addition to FSC and SSC, 5 fluorescence channels: CD3, CD4, CD8, CD69 and HLADR.
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immunooncologyworkflowworkflowproteomicsworkflow
2.30 scoreyeastNagalakshmi - Yeast genome RNA sequencing data based on Nagalakshmi et. al.
The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools.
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experimentdatagenomesaccharomyces_cerevisiae_datasequencingdatabiocviewschipseqdatadatapkg
2.30 scorehgu2beta7 - A data package containing annotation data for hgu2beta7
Annotation data file for hgu2beta7 assembled using data from public data repositories
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genomedatapkg
2.30 score 3 scriptsannotation - Genomic Annotation Resources
Annotation resources make up a significant proportion of the Bioconductor project. And there are also a diverse set of online resources available which are accessed using specific packages. This walkthrough will describe the most popular of these resources and give some high level examples on how to use them.
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annotationworkflowworkflow
1.48 score