Package: recount 1.39.0

Leonardo Collado-Torres

recount: Explore and download data from the recount project

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

Authors:Leonardo Collado-Torres [aut, cre], Abhinav Nellore [ctb], Andrew E. Jaffe [ctb], Margaret A. Taub [ctb], Kai Kammers [ctb], Shannon E. Ellis [ctb], Kasper Daniel Hansen [ctb], Ben Langmead [ctb], Jeffrey T. Leek [aut, ths]

recount_1.39.0.tar.gz
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recount_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
recount/json (API)

# Install 'recount' in R:
install.packages('recount', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/leekgroup/recount/issues

Datasets:

On BioConductor:recount-1.39.0(bioc 3.24)recount-1.38.0(bioc 3.23)

coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportimmunooncologyannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecount

9.55 score 41 stars 4 packages 588 scripts 1.0k downloads 18 exports 155 dependencies

Last updated from:a492ff2d65. Checks:6 ERROR, 4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR291
linux-develOK724
source / vignettesOK544
linux-releaseOK634
macos-releaseERROR577
macos-oldrelERROR397
windows-develERROR443
windows-releaseERROR600
windows-oldrelERROR537
wasm-releaseOK211

Exports:abstract_searchadd_metadataadd_predictionsall_metadatabrowse_studycoverage_matrixdownload_retrydownload_studyexpressed_regionsfind_geogeo_characteristicsgeo_infogetRPKMgetTPMread_countsreproduce_rangesscale_countssnaptron_query

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibbumphuntercachemcheckmatecigarilloclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayderfinderderfinderHelperdigestdoRNGdownloaderdplyrevaluatefarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesGEOqueryggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpillarpkgconfigplyrpngprettyunitsprogresspurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8VariantAnnotationvctrsviridisLitevroomwithrxfunXMLxml2XVectoryaml

recount quick start guide
Basics | Install r Biocpkg('recount') | Required knowledge | Asking for help | Workflow using r Biocpkg('recount') | Citing r Biocpkg('recount') | Quick start to using to r Biocpkg('recount') | Introduction | Sample DE analysis | Download data | Finding phenotype information | Predicted phenotype information | DE analysis | Report results | Finding gene names | Sample r Biocpkg('derfinder') analysis | Define expressed regions | Compute coverage matrix | Construct a DESeqDataSet object | r Biocpkg('DESeq2') analysis | Annotation used | Using another/newer annotation | Candidate gene fusions | Snaptron | FANTOM-CAT annotation | recount-brain | Download all the data | Accessing r Biocpkg('recount') via SciServer | Step by step | SciServer help | Citing SciServer | Reproducibility | Bibliography
Rendered fromrecount-quickstart.Rmdusingknitr::rmarkdown

Last update: 2024-12-12
Started: 2016-05-04

Basic DESeq2 results exploration
Rendered fromSRP009615-results.Rmdusing

Last update: ??
Started: ??

Readme and manuals

Help Manual

Help pageTopics
Search the abstracts from the SRA studies available via the recount projectabstract_search
Add additional curated metadata to a recount rse objectadd_metadata
Add predicted phenotypes to a recount rse objectadd_predictions
This function downloads the metadata for all projects.all_metadata
Open a SRA study id in the SRA websitebrowse_study
Given a set of regions for a chromosome, compute the coverage matrix for a given SRA study.coverage_matrix
Retry multiple times to download a filedownload_retry
Download data for a given SRA study id from the recount projectdownload_study
Identify expressed regions from the mean coverage for a given SRA projectexpressed_regions
Find the GEO accession id for a given SRA runfind_geo
Build a data.frame from GEO's charactersitics for a given samplegeo_characteristics
Extract information from GEO for a given samplegeo_info
Compute an RPKM matrix based on a RangedSummarizedExperiment objectgetRPKM
Compute a TPM matrix based on a RangedSummarizedExperiment objectgetTPM
Compute read countsread_counts
Summary information at the project level for the recount projectrecount_abstract
Exon annotation used in recountrecount_exons
Gene annotation used in recountrecount_genes
Files and URLs hosted by the recount projectrecount_url
Reproduce the gene or exons used in the RangedSummarizedExperiment objectsreproduce_ranges
RangedSummarizedExperiment at the gene level for study SRP009615rse_gene_SRP009615
Scale the raw counts provided by the recount projectscale_counts
Query Snaptron to get data from exon-exon junctions present in Intropolissnaptron_query