Package: fCI 1.35.0

Shaojun Tang

fCI: f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics

(f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.

Authors:Shaojun Tang

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fCI.pdf |fCI.html✨
fCI/json (API)

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

Peer review:

Datasets:

On BioConductor:fCI-1.35.0(bioc 3.20)fCI-1.34.0(bioc 3.19)

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

bioconductor-package

35 exports 1.00 score 42 dependencies

Last updated 2 months agofrom:323dd4850f

Exports:call.npcicomputedeg.pairwise.fold.changedeg.up.down.infodeseq.median.ratio.normalizationdivergence.multivariate.distributionsfCI.call.by.indexfiguresfind.fci.targetsfind.mid.pointget.fold.large.stepget.npci.dataget.npci.distance.matrixget.outline.indexget.protein.fold.stepget.rank.combinationsget.rna.fold.stepintersect.of.listsis.installednormalizationnpci.gene.by.pvaluesnpci.index.reconsiderednpci.index.to.be.removednpci.venn.diagrampairwise.change.occupancypopulatereport.target.summarysetfCIshow.targetssummarizetotal.library.size.normalizationtrim.size.normalizationtwo.sample.log.ratiotwo.sample.permutation.testvenndiagram

Dependencies:base64encbslibcachemclidigestevaluatefastmapFNNfontawesomeformatRfsfutile.loggerfutile.optionsglueGPArotationgtoolshighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlambda.rlatticelifecyclemagrittrmemoisemimemnormtnlmepsychR6rappdirsrglrlangrmarkdownsasstinytexVennDiagramxfunyamlzoo

fCI

Rendered fromfCI.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2018-08-30
Started: 2015-06-17

Readme and manuals

Help Manual

Help pageTopics
the s4 class functioncall.npci
~~ Methods for Function 'call.npci' ~~call.npci,NPCI-method call.npci-methods
the generic function 'compute' for s4 classcompute
~~ Methods for Function 'compute' ~~compute,NPCI-method compute-methods
find targets that have a consistent fold change in the same direction (either up- or down-regulation)deg.pairwise.fold.change
find targets and their detailed expression changesdeg.up.down.info
data matrix normalization methoddeseq.median.ratio.normalization
estimate fCI divergence for given samples of aritrary dimensionsdivergence.multivariate.distributions
Class '"fCI"'fCI-class
top level function call to find targets based on expression data and control & case indexesfCI.call.by.index
data frame of gene expressionfci.data
generic function to draw figures of the current analysisfigures
generate figures for empirical null and case-control distributionsfigures,NPCI-method figures-methods
identify differentially expressed genesfind.fci.targets
~~ Methods for Function 'find.fci.targets' ~~find.fci.targets,NPCI-method find.fci.targets-methods
find the middle value of the density distributionfind.mid.point
generate fold change cutoff values for fCI divergence computationget.fold.large.step
return a fCI object given the gene expression dataget.npci.data
generate the divergence estimation based of fold change cutoff valuesget.npci.distance.matrix
find the outline genes of a given distributionget.outline.index
generate fold-change cutoff on proteomics data (with large steps of 0.2-0.5 fold)get.protein.fold.step
fold change valuesget.rank.combinations
generate fCI fold-change cutoff values for typical RNA-Seq dataget.rna.fold.step
~~ Methods for Function 'initialize' ~~initialize,NPCI-method initialize-methods
find the common values of all vectors of a listintersect.of.lists
packageis.installed
data frame of gene expressionmulti.dimensional.fci.data
generic function to normalize gene expression matrixnormalization
~~ Methods for Function 'normalization' ~~normalization,NPCI-method normalization-methods
Class '"NPCI"'NPCI-class
find most signficantly change fCI targetsnpci.gene.by.pvalues
find targets that have little evidence to be differentially expressednpci.index.reconsidered
gene indexes that will be considered as targetsnpci.index.to.be.removed
generate venn diagram for multiple fCI analysisnpci.venn.diagram
find the targets whose fold changes occur consistently (upregulated or downregulated) in all fCI analysispairwise.change.occupancy
generic function to populate the fCI object based on provided datapopulate
~~ Methods for Function 'populate' ~~populate,NPCI-method populate-methods
generate the results (gene ids) in the data framereport.target.summary
the generic function 'setfCI' for s4 classsetfCI
~~ Methods for Function 'setfCI' ~~setfCI,NPCI-method setfCI-methods
display the gene ids that are identified to be differentially regulatedshow.targets
~~ Methods for Function 'show.targets' ~~show.targets,NPCI-method show.targets-methods
result summerizationsummarize
result summerizationsummarize,NPCI-method summarize-methods
normalize the gene expression based on the library size (summation) of the first sample replicatetotal.library.size.normalization
normalize gene expression by exluding genes on the top 5 and bottom 5 percentagetrim.size.normalization
compute the log ratios of two vectorstwo.sample.log.ratio
perform permuation test on two vectorstwo.sample.permutation.test
generate a venn diagram to show the differentially expression summaries accross pairwise fCI analysisvenndiagram
~~ Methods for Function 'venndiagram' ~~venndiagram,NPCI-method venndiagram-methods