Package: recount 1.31.2

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_1.31.2.tar.gz
recount_1.31.2.zip(r-4.5)recount_1.31.2.zip(r-4.4)recount_1.31.2.zip(r-4.3)
recount_1.31.2.tgz(r-4.4-any)recount_1.31.2.tgz(r-4.3-any)
recount_1.31.2.tar.gz(r-4.5-noble)recount_1.31.2.tar.gz(r-4.4-noble)
recount_1.31.2.tgz(r-4.4-emscripten)recount_1.31.2.tgz(r-4.3-emscripten)
recount.pdf |recount.html✨
recount/json (API)
NEWS

# 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:

recount_abstract - Summary information at the project level for the recount project
recount_exons - Exon annotation used in recount
recount_genes - Gene annotation used in recount
recount_url - Files and URLs hosted by the recount project
rse_gene_SRP009615 - RangedSummarizedExperiment at the gene level for study SRP009615

On BioConductor:recount-1.31.2(bioc 3.20)recount-1.30.2(bioc 3.19)

bioconductor-package

18 exports 1.58 score 154 dependencies 3 dependents

Last updated 2 months agofrom:f4d2db9cff

Exports:abstract_search add_metadata add_predictions all_metadata browse_study coverage_matrix download_retry download_study expressed_regions find_geo geo_characteristics geo_info getRPKM getTPM read_counts reproduce_ranges scale_counts snaptron_query

Dependencies:abind AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib bumphunter cachem checkmate cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray derfinder derfinderHelper digest doRNG downloader dplyr evaluate fansi farver fastmap fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges GEOquery ggplot2 glue gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr plyr png prettyunits progress purrr qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape2 restfulr Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 XVector yaml zlibbioc

Basic DESeq2 results exploration

Rendered fromSRP009615-results.Rmdusingon Jun 21 2024.

Last update: ??
Started: ??

recount quick start guide

Leonardo Collado-Torres

Rendered fromrecount-quickstart.Rmdusingknitr::rmarkdownon Jun 21 2024.

Last update: 2024-05-21
Started: 2016-05-04

Help page	Topics
Search the abstracts from the SRA studies available via the recount project	abstract_search
Add additional curated metadata to a recount rse object	add_metadata
Add predicted phenotypes to a recount rse object	add_predictions
This function downloads the metadata for all projects.	all_metadata
Open a SRA study id in the SRA website	browse_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 file	download_retry
Download data for a given SRA study id from the recount project	download_study
Identify expressed regions from the mean coverage for a given SRA project	expressed_regions
Find the GEO accession id for a given SRA run	find_geo
Build a data.frame from GEO's charactersitics for a given sample	geo_characteristics
Extract information from GEO for a given sample	geo_info
Compute an RPKM matrix based on a RangedSummarizedExperiment object	getRPKM
Compute a TPM matrix based on a RangedSummarizedExperiment object	getTPM
Compute read counts	read_counts
Summary information at the project level for the recount project	recount_abstract
Exon annotation used in recount	recount_exons
Gene annotation used in recount	recount_genes
Files and URLs hosted by the recount project	recount_url
Reproduce the gene or exons used in the RangedSummarizedExperiment objects	reproduce_ranges
RangedSummarizedExperiment at the gene level for study SRP009615	rse_gene_SRP009615
Scale the raw counts provided by the recount project	scale_counts
Query Snaptron to get data from exon-exon junctions present in Intropolis	snaptron_query

Package: recount 1.31.2

recount: Explore and download data from the recount project

Basic DESeq2 results exploration

recount quick start guide

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)