Package: CHRONOS 1.41.0

Panos Balomenos

CHRONOS: CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.

Authors:Aristidis G. Vrahatis, Konstantina Dimitrakopoulou, Panos Balomenos

CHRONOS_1.41.0.tar.gz
CHRONOS_1.41.0.zip(r-4.7)CHRONOS_1.41.0.zip(r-4.6)CHRONOS_1.41.0.zip(r-4.5)
CHRONOS_1.41.0.tgz(r-4.6-any)CHRONOS_1.41.0.tgz(r-4.5-any)
CHRONOS_1.41.0.tar.gz(r-4.7-any)CHRONOS_1.41.0.tar.gz(r-4.6-any)
CHRONOS_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CHRONOS/json (API)

# Install 'CHRONOS' in R:

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

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:CHRONOS-1.41.0(bioc 3.24)CHRONOS-1.40.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

systemsbiology graphandnetwork pathways kegg openjdk

4.01 score 17 scripts 3 mentions 16 exports 77 dependencies

Last updated from:4da19ef004. Checks:3 ERROR, 5 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	181
linux-devel-x86_64	NOTE	321
source / vignettes	OK	246
linux-release-x86_64	NOTE	271
macos-release-arm64	ERROR	317
macos-oldrel-arm64	ERROR	428
windows-devel	NOTE	197
windows-release	NOTE	203
windows-oldrel	NOTE	185
wasm-release	OK	194

Exports:CHRONOSrun convertMiRNANomenclature convertNomenclature createPathwayGraphs downloadKEGGPathwayList downloadMiRecords downloadPathways extractLinearSubpathways extractNonLinearSubpathways getEdgeTypes importExpressions pathwayMeasures scoreSubpathways subpathwayKEGGmap subpathwayMiRNAs visualizeResults

Dependencies:AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 bitops blob cachem circlize cli codetools colorspace cpp11 crayon curl DBI dbplyr doParallel dplyr fastmap filelock foreach generics GlobalOptions glue graph hms httr httr2 igraph IRanges iterators jsonlite KEGGREST lattice lifecycle magrittr Matrix memoise mime openssl openxlsx pillar pkgconfig png prettyunits progress purrr R6 rappdirs RBGL Rcpp RCurl rJava rlang RSQLite S4Vectors Seqinfo shape stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr XML xml2 XVector zip

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

Table of Contents | Package Setup | User Input | Default Run | Citation

Rendered fromCHRONOS.Rmdusingknitr::rmarkdown

Last update: 2017-04-05
Started: 2016-04-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Default run of CHRONOS	CHRONOSrun
Conform miRNA annotations to the ones currently used by miRecords.	convertMiRNANomenclature
Convert genes identifier nomenclature.	convertNomenclature
Convert KEGG Pathways to Gene-Gene Network Graphs.	createPathwayGraphs
Retrieve all availiable pathways for an organism.	downloadKEGGPathwayList
Download miRNA-mRNA interactions for an organism.	downloadMiRecords
Download KEGG pathways in KGML format.	downloadPathways
Linear subpathway extraction from pathway graphs	extractLinearSubpathways
Non linear subpathway extraction from pathway graphs	extractNonLinearSubpathways
Map various types of gene-gene interactions in KGML files to edge types in corresponding pathway graphs.	getEdgeTypes
Import gene and miRNA expressions from	importExpressions
Pathway structural and functional aspects	pathwayMeasures
Evaluate subpathways using an interacting scorng scheme (IS) for each time point.	scoreSubpathways
Create links to KEGG pathway map with highlighted subpathways.	subpathwayKEGGmap
Create a circulat plot of a subpathway and the miRNAs that target it.	subpathwayMiRNAs
Visualize results in tabular form (txt, xlsx)	visualizeResults