ACME: Algorithms for Calculating Microarray Enrichment (ACME)
Version 2.32.0

ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

AuthorSean Davis <sdavis2@mail.nih.gov>
Bioconductor views Microarray Normalization Technology
Date of publicationNone
MaintainerSean Davis <sdavis2@mail.nih.gov>
LicenseGPL (>= 2)
Version2.32.0
URL http://watson.nci.nih.gov/~sdavis
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ACME")

Popular man pages

aGFFCalc-class: Class "aGFFCalc"
aGFF-class: Class for storing GFF-like data
example.agff: An example ACME data structure of class ACMESet
findClosestGene: Find closest refseq gene
findRegions: Find all regions in data above p-value threshold
getRefflat: Get the refflat table from ucsc for the given genome
write.sgr: Write Affy IGB .sgr format files
See all...

All man pages Function index File listing

Man pages

ACMECalcSet-class: Class "ACMECalcSet"
ACMESet-class: Class "ACMESet"
aGFFCalc-class: Class "aGFFCalc"
aGFF-class: Class for storing GFF-like data
do.aGFF.calc: Perform ACME calculation
example.agff: An example ACME data structure of class ACMESet
findClosestGene: Find closest refseq gene
findRegions: Find all regions in data above p-value threshold
generics: Generics defined within ACME
getRefflat: Get the refflat table from ucsc for the given genome
read.resultsGFF: Read Nimblegen GFF files
write.bedGraph: Write bedGraph format tracks for UCSC genome browser
write.sgr: Write Affy IGB .sgr format files

Functions

ACMECalcSet-class Man page
ACMESet-class Man page
aGFF-class Man page
aGFFCalc-class Man page
chromosome Man page
chromosome,ACMESet-method Man page
cutpoints Man page
cutpoints,ACMECalcSet-method Man page
do.aGFF.calc Man page
end Man page
end,ACMESet-method Man page
example.agff Man page
findClosestGene Man page
findRegions Man page
getRefflat Man page
plot Man page
plot,ACMECalcSet-method Man page
plot,ACMESet-method Man page
plot,aGFF-method Man page
plot,aGFFCalc-method Man page
plotACMECalcSet Source code
plotACMESet Source code
plotgff Source code
plotgffcalc Source code
print,aGFF-method Man page
print,aGFFCalc-method Man page
printgff Source code
printgffcalc Source code
read.resultsGFF Man page
show,ACMECalcSet-method Man page
show,aGFF-method Man page
show,aGFFCalc-method Man page
start Man page
start,ACMESet-method Man page
threshold Man page
threshold,ACMECalcSet-method Man page
vals Man page
vals,ACMECalcSet-method Man page
windowChisq Source code
write.bedGraph Man page Source code
write.sgr Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/Classes.R
R/do.aGFF.calc.R
R/findClosestGene.R
R/findRegions.R
R/getRefflat.R
R/read.resultsGFF.R
R/write.bedGraph.R
R/write.sgr.R
build
build/vignette.rds
data
data/datalist
data/example.agff.rda
inst
inst/CITATION
inst/doc
inst/doc/ACME.R
inst/doc/ACME.Rnw
inst/doc/ACME.pdf
inst/extdata
inst/extdata/testsamp1.gff
inst/extdata/testsamp2.gff
man
man/ACMECalcSet-class.Rd
man/ACMESet-class.Rd
man/aGFF-class.Rd
man/aGFFCalc-class.Rd
man/do.aGFF.calc.Rd
man/example.agff.Rd
man/findClosestGene.Rd
man/findRegions.Rd
man/generics.Rd
man/getRefflat.Rd
man/read.resultsGFF.Rd
man/write.bedGraph.Rd
man/write.sgr.Rd
src
src/windowChisq.c
vignettes
vignettes/ACME.Rnw
ACME documentation built on May 20, 2017, 10:30 p.m.