Package: ADAM 1.29.0

Jose Luiz Rybarczyk Filho

ADAM: ADAM: Activity and Diversity Analysis Module

ADAM is a GSEA R package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions (Gene Ontology and KEGG pathways as default) and show their significance by calculating p-values referring togene diversity and activity. Each group of genes is called GFAG (Group of Functionally Associated Genes).

Authors:André Luiz Molan [aut], Giordano Bruno Sanches Seco [ctb], Agnes Takeda [ctb], Jose Rybarczyk Filho [ctb, cre, ths]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ADAM/json (API)

# Install 'ADAM' in R:

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

ExpressionAedes - Aedes aegypti RNA-seq data expression
KeggPathwaysAedes - Relation between Aedes aegypti genes and KEGG pathways as ADAM input

On BioConductor:ADAM-1.29.0(bioc 3.24)ADAM-1.28.0(bioc 3.23)

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

genesetenrichment pathways kegg geneexpression microarray cpp

4.89 score 1 packages 13 scripts 482 mentions 2 exports 80 dependencies

Last updated from:8f82406121. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	194
linux-devel-arm64	NOTE	268
linux-devel-x86_64	NOTE	325
source / vignettes	OK	278
linux-release-arm64	NOTE	271
linux-release-x86_64	NOTE	323
macos-release-arm64	NOTE	188
macos-release-x86_64	NOTE	483
macos-oldrel-arm64	NOTE	205
macos-oldrel-x86_64	NOTE	413
windows-devel	NOTE	467
windows-release	NOTE	413
windows-oldrel	NOTE	478
wasm-release	OK	287

Exports:ADAnalysis GFAGAnalysis

Dependencies:abind AnnotationDbi askpass base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem cli cpp11 crayon crosstalk curl DBI DelayedArray digest dplyr DT evaluate fastmap fontawesome fs generics GenomicRanges glue GO.db highr htmltools htmlwidgets httr IRanges jquerylib jsonlite KEGGREST knitr later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pbapply pillar pkgconfig png promises R6 rappdirs Rcpp rlang rmarkdown RSQLite S4Arrays S4Vectors sass Seqinfo SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect tinytex utf8 vctrs withr xfun XVector yaml

ADAM: Activity and Diversity Analysis Module

Overview | GFAGAnalysis | ADAnalysis | Session information | References

Rendered fromADAM.Rmdusingknitr::rmarkdown

Last update: 2021-09-01
Started: 2018-10-05

Help page	Topics
Group of Functionally Associated Genes (GFAG) partial analysis	ADAnalysis
Aedes aegypti RNA-seq data expression	ExpressionAedes
Group of Functionally Associated Genes (GFAG) complete analysis	GFAGAnalysis
Relation between Aedes aegypti genes and KEGG pathways as ADAM input	KeggPathwaysAedes

Package: ADAM 1.29.0

ADAM: ADAM: Activity and Diversity Analysis Module

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)