ACME: Algorithms for Calculating Microarray Enrichment (ACME)

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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.

Author
Sean Davis <sdavis2@mail.nih.gov>
Date of publication
None
Maintainer
Sean Davis <sdavis2@mail.nih.gov>
License
GPL (>= 2)
Version
2.30.0
URLs

View on Bioconductor

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

Files in this package

ACME/DESCRIPTION
ACME/NAMESPACE
ACME/R
ACME/R/Classes.R
ACME/R/do.aGFF.calc.R
ACME/R/findClosestGene.R
ACME/R/findRegions.R
ACME/R/getRefflat.R
ACME/R/read.resultsGFF.R
ACME/R/write.bedGraph.R
ACME/R/write.sgr.R
ACME/build
ACME/build/vignette.rds
ACME/data
ACME/data/datalist
ACME/data/example.agff.rda
ACME/inst
ACME/inst/CITATION
ACME/inst/doc
ACME/inst/doc/ACME.R
ACME/inst/doc/ACME.Rnw
ACME/inst/doc/ACME.pdf
ACME/inst/extdata
ACME/inst/extdata/testsamp1.gff
ACME/inst/extdata/testsamp2.gff
ACME/man
ACME/man/ACMECalcSet-class.Rd
ACME/man/ACMESet-class.Rd
ACME/man/aGFF-class.Rd
ACME/man/aGFFCalc-class.Rd
ACME/man/do.aGFF.calc.Rd
ACME/man/example.agff.Rd
ACME/man/findClosestGene.Rd
ACME/man/findRegions.Rd
ACME/man/generics.Rd
ACME/man/getRefflat.Rd
ACME/man/read.resultsGFF.Rd
ACME/man/write.bedGraph.Rd
ACME/man/write.sgr.Rd
ACME/src
ACME/src/windowChisq.c
ACME/vignettes
ACME/vignettes/ACME.Rnw