Package: RevEcoR 0.99.3

RevEcoR: Reverse Ecology Analysis on Microbiome

An implementation of the reverse ecology framework. Reverse ecology refers to the use of genomics to study ecology with no a priori assumptions about the organism(s) under consideration, linking organisms to their environment. It allows researchers to reconstruct the metabolic networks and study the ecology of poorly characterized microbial species from their genomic information, and has substantial potentials for microbial community ecological analysis.

Authors:Yang Cao [aut, cre]

RevEcoR_0.99.3.tar.gz
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RevEcoR.pdf |RevEcoR.html✨
RevEcoR/json (API)

# Install 'RevEcoR' in R:
install.packages('RevEcoR', repos = c('https://yiluheihei.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/yiluheihei/revecor/issues

Datasets:
  • RefDbcache - Reference data for global metabolic construction The reference metabolic pathway data contains KOs, substrates and products, as well as a constructed reference global network, which used for metabolic network reconstruction
  • anno.species - Annotation profiles of seven well-studied oral species
  • gut_microbiome - Annotation profiles of 116 gut prevalent species
  • kegg_buc - Metabolic profiles of KEGG organism Buchnera aphidicola APS
  • kegg_ptr - Metabolic profiles of KEGG organism Pan troglodytes

On CRAN:

5.77 score 6 stars 1 packages 22 scripts 147 downloads 3 mentions 15 exports 18 dependencies

Last updated 5 years agofrom:cedbfeb1b4. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winNOTEOct 27 2024
R-4.5-linuxNOTEOct 27 2024
R-4.4-winNOTEOct 27 2024
R-4.4-macNOTEOct 27 2024
R-4.3-winNOTEOct 27 2024
R-4.3-macNOTEOct 27 2024

Exports:%.%calculateCooperationIndexcompetitionIndexcomplementarityIndexcomposeconfidencescoregetGsMNgetOrgMetabolicDatagetSeedSetsKosarajuSCClennonseedreconstructGsMNseedSizeshow

Dependencies:clicpp11gluegtoolsigraphlatticelifecyclemagrittrMatrixpkgconfigplyrpurrrRcpprlangstringistringrvctrsXML

Revse Ecology Analysis on Microbiome

Rendered fromRevEcoR.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2016-11-21
Started: 2014-09-26

Readme and manuals

Help Manual

Help pageTopics
Annotation profiles of seven well-studied oral speciesanno.species
Calculating the metabolic competition and complementarity indexcalculateCooperationIndex
Compose multiple functions%.% compose
Conficence scoreconfidencescore confidencescore,seedset-method confidencescore-methods
The genome scale metabolic networkgetGsMN getGsMN,seedset-method getGsMN-methods
Get organism metabolic data from KEGG databasegetOrgMetabolicData
Identify seed compounds of each organismgetSeedSets
Annotation profiles of 116 gut prevalent speciesgut_microbiome
Calculating the species interactionscompetitionIndex complementarityIndex Interactions
Metabolic profiles of KEGG organism Buchnera aphidicola APS (Acyrthosiphon pisum) (KEGG organism code: buc)kegg_buc
Metabolic profiles of KEGG organism Pan troglodytes (chimpanzee) (KEGG organism code: ptr)kegg_ptr
Caculating the strong connected components (SCC) of a networkKosarajuSCC
the length of the seed setlen len,seedset-method len-methods
Non seed of the networknonseed nonseed,seedset-method nonseed-methods
Reconstuction of the specific-organism genome-scale metabolic networkreconstructGsMN
Reference data for global metabolic construction The reference metabolic pathway data contains KOs, substrates and products, as well as a constructed reference global network, which used for metabolic network reconstructionRefDbcache
The RevEcoR packageRevEcoR-package RevEcoR
'seedset-class'seedset-class
Size of the each seed source componentseedSize seedSize,seedset-method seedSize-methods
The show generic functionshow show,seedset-method show-methods