Package: regutools 1.17.0

Joselyn Chavez

regutools: regutools: an R package for data extraction from RegulonDB

RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.

Authors:Joselyn Chavez [aut, cre], Carmina Barberena-Jonas [aut], Jesus E. Sotelo-Fonseca [aut], Jose Alquicira-Hernandez [ctb], Heladia Salgado [ctb], Leonardo Collado-Torres [aut], Alejandro Reyes [aut]

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NEWS

# Install 'regutools' in R:

install.packages('regutools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/comunidadbioinfo/regutools/issues

On BioConductor:regutools-1.17.0(bioc 3.20)regutools-1.16.0(bioc 3.19)

bioconductor-package

19 exports 1.08 score 163 dependencies

Last updated 2 months agofrom:0e8dd206ce

Exports:build_condition connect_database convert_to_biostrings convert_to_granges existing_intervals existing_partial_match get_binding_sites get_dataset get_dna_objects get_gene_regulators get_gene_synonyms get_regulatory_network get_regulatory_summary guess_id list_attributes list_datasets non_existing_intervals plot_dna_objects regulondb

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64enc base64url BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem caTools checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gplots graph gridExtra gtable gtools Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges IRdisplay IRkernel isoband jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pbdZMQ pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl RCy3 repr restfulr Rhtslib rjson RJSONIO rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 uuid VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

regutools: an R package for the extraction of gene regulatory networks from RegulonDB

Joselyn Chávez, Carmina Barberena Jonas, Jesus Emiliano Sotelo-Fonseca, Jose Alquicira Hernandez, Heladia Salgado, Leonardo Collado-Torres, Alejandro Reyes

Rendered fromregutools.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2020-12-18
Started: 2017-06-05

Help page	Topics
Construct logical condition to query database	build_condition
Connect to the regulondb database	connect_database
Function to convert output of regulondb queries to Biostrings objects	convert_to_biostrings
Function to convert output of regulondb queries to GenomicRanges objects	convert_to_granges
Constructs a particular logical condition to query database	existing_intervals
Constructs a logical condition to query database	existing_partial_match
Get the binding sites for a Transcription Factor (TF)	get_binding_sites
Extract data from RegulonDB	get_dataset
Retrieve genomic elements from regulonDB	get_dna_objects
Get TFs or genes that regulate the genes of interest	get_gene_regulators
Retrieve gene synonyms	get_gene_synonyms
Return complete regulatory network.	get_regulatory_network
Return summary of gene regulation.	get_regulatory_summary
Guess gene id type	guess_id
List attributes/fields from a dataset/table	list_attributes
List available datasets in RegulonDB database	list_datasets
Constructs a logical condition to query database	non_existing_intervals
Plot annotation elements within genomic region	plot_dna_objects
Constructor function of a regulondb class	build_regulondb regulondb
The regulondb_results class	regulondb_result-class
The regulondb class	regulondb-class
Methods for regulondb objects	show show,regulondb-method

Package: regutools 1.17.0

regutools: regutools: an R package for data extraction from RegulonDB

regutools: an R package for the extraction of gene regulatory networks from RegulonDB

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