Package: RITAN 1.37.0

Michael Zimmermann

RITAN: Rapid Integration of Term Annotation and Network resources

Tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research.

Authors:Michael Zimmermann [aut, cre]

RITAN_1.37.0.tar.gz
RITAN_1.37.0.zip(r-4.7-any)RITAN_1.37.0.zip(r-4.6-any)RITAN_1.37.0.zip(r-4.5-any)
RITAN_1.37.0.tgz(r-4.6-any)RITAN_1.37.0.tgz(r-4.5-any)
RITAN_1.37.0.tar.gz(r-4.7-any)RITAN_1.37.0.tar.gz(r-4.6-any)
RITAN_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RITAN/json (API)

# Install 'RITAN' in R:

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

Datasets:

vac1.day0vs31.de.genes - This dataset is included as an example in the package:
vac1.day0vs56.de.genes - This dataset is included as an example in the package:
vac2.day0vs31.de.genes - This dataset is included as an example in the package:
vac2.day0vs56.de.genes - This dataset is included as an example in the package:

On BioConductor:RITAN-1.37.0(bioc 3.24)RITAN-1.36.0(bioc 3.23)

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

qualitycontrol network networkenrichment networkinference genesetenrichment functionalgenomics graphandnetwork

5.70 score 20 scripts 484 downloads 5 mentions 16 exports 147 dependencies

Last updated from:f3a935df74. Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	304
linux-devel	WARNING	516
source / vignettes	ERROR	495
linux-release	WARNING	390
macos-release	WARNING	396
macos-oldrel	WARNING	306
windows-devel	WARNING	516
windows-release	WARNING	336
windows-oldrel	WARNING	326
wasm-release	OK	263

Exports:as.graph check_any_net_input check_net_input enrichment_symbols geneset_overlap icon_test load_geneset_symbols network_overlap readGMT readSIF resource_reduce show_active_genesets_hist term_enrichment term_enrichment_by_subset write_simple_table writeGMT

Dependencies:abind anndata AnnotationDbi AnnotationFilter askpass assertthat basilisk BgeeDB BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob bread cachem caTools chron cigarillo cli codetools cpp11 crayon curl data.table DBI DelayedArray digest dir.expiry dplyr dynamicTreeCut EnsDb.Hsapiens.v86 ensembldb evaluate expm farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue GO.db gplots graph gridExtra gsubfn gtable gtools h5mread hash HDF5Array here highr httr igraph IRanges isoband jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats MCL memoise mime openssl pillar pkgconfig plotrix plyr png ProtGenerics proto purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppTOML RCurl reshape2 restfulr reticulate rhdf5 rhdf5filters Rhdf5lib Rhtslib RITANdata rjson rlang rprojroot Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment snow SparseArray SparseM sqldf STRINGdb stringi stringr SummarizedExperiment sys tibble tidyr tidyselect topGO UCSC.utils utf8 vctrs viridisLite withr xfun XML XVector yaml zellkonverter

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Enrichment Vignette

Rendered fromenrichment.Rmdusingknitr::rmarkdown

Last update: 2020-02-18
Started: 2017-03-03

Multi-Tissue Analysis

Enrichment to Identify Tissue-Specific Patterns

Rendered frommulti_tissue_analysis.Rmdusingknitr::rmarkdown

Last update: 2018-08-30
Started: 2017-09-20

Network Biology (Induced Subnetwork) Vignette

Rendered fromsubnetworks.Rmdusingknitr::rmarkdown

Last update: 2018-08-13
Started: 2017-03-03

Choosing Resources

Resources Indexed by default | Example: Protein Complexes & Protein-Protein Interaction (PPI) | Example: Metabolic Network Interaction | Example: Expression Signalling

Rendered fromchoosing_resources.Rmdusingknitr::rmarkdown

Last update: 2018-08-07
Started: 2017-09-20

Relationships Among Resources

Identify relationships between genesets

Rendered fromresource_relationships.Rmdusingknitr::rmarkdown

Last update: 2018-03-09
Started: 2017-09-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
as.graph	as.graph
check_any_net_input	check_any_net_input
check_net_input	check_net_input
cov_undirected function to show the un-directed coverabe between two nodes lists from two networks	cov_undirected
enrichment_symbols	enrichment_symbols
geneset_overlap	geneset_overlap
icon_single_within interconnectivity score within a network	icon_single_within
icon_test	icon_test
load_all_protein_coding_symbols	load_all_protein_coding_symbols
load_geneset_symbols	load_geneset_symbols
network_overlap	network_overlap
plot.term_enrichment	plot.term_enrichment
plot.term_enrichment_by_subset	plot.term_enrichment_by_subset
readGMT	readGMT
readSIF	readSIF
resource_reduce Merge terms across resources to reduce the number of redundant and semi-redundant terms	resource_reduce
show_active_genesets_hist	show_active_genesets_hist
summary.term_enrichment	summary.term_enrichment
summary.term_enrichment_by_subset	summary.term_enrichment_by_subset
term_enrichment	term_enrichment
term_enrichment_by_subset	term_enrichment_by_subset
This dataset is included as an example in the package:	vac1.day0vs31.de.genes
This dataset is included as an example in the package:	vac1.day0vs56.de.genes
This dataset is included as an example in the package:	vac2.day0vs31.de.genes
This dataset is included as an example in the package:	vac2.day0vs56.de.genes
write_simple_table	write_simple_table
writeGMT	writeGMT