Overview of ACME | Getting Started using ACME
Package: ACME 2.69.0
Sean Davis
ACME: Algorithms for Calculating Microarray Enrichment (ACME)
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.
Authors:
ACME_2.69.0.tar.gz
ACME_2.69.0.zip(r-4.7)ACME_2.69.0.zip(r-4.6)ACME_2.69.0.zip(r-4.5)
ACME_2.69.0.tgz(r-4.6-x86_64)ACME_2.69.0.tgz(r-4.6-arm64)ACME_2.69.0.tgz(r-4.5-x86_64)ACME_2.69.0.tgz(r-4.5-arm64)
ACME_2.69.0.tar.gz(r-4.7-arm64)ACME_2.69.0.tar.gz(r-4.7-x86_64)ACME_2.69.0.tar.gz(r-4.6-arm64)ACME_2.69.0.tar.gz(r-4.6-x86_64)
ACME_2.69.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ACME/json (API)
| # Install 'ACME' in R: |
| install.packages('ACME', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/seandavi/acme/issues
Datasets:
- example.agff - An example ACME data structure of class ACMESet
On BioConductor:ACME-2.69.0(bioc 3.24)ACME-2.68.0(bioc 3.23)
technologymicroarraynormalization
Last updated from:bbcf640bdc. Checks:12 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 145 | ||
| linux-devel-arm64 | WARNING | 155 | ||
| linux-devel-x86_64 | WARNING | 160 | ||
| source / vignettes | OK | 201 | ||
| linux-release-arm64 | WARNING | 142 | ||
| linux-release-x86_64 | WARNING | 164 | ||
| macos-release-arm64 | WARNING | 128 | ||
| macos-release-x86_64 | WARNING | 174 | ||
| macos-oldrel-arm64 | WARNING | 91 | ||
| macos-oldrel-x86_64 | WARNING | 247 | ||
| windows-devel | WARNING | 97 | ||
| windows-release | WARNING | 98 | ||
| windows-oldrel | WARNING | 105 | ||
| wasm-release | OK | 107 |
Exports:chromosomecutpointsdo.aGFF.calcendfindClosestGenefindRegionsgetRefflatplotprintread.resultsGFFshowstartthresholdvalswrite.bedGraphwrite.sgr
Dependencies:BiobaseBiocGenericsgenerics
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class "ACMECalcSet" | ACMECalcSet-class cutpoints,ACMECalcSet-method plot,ACMECalcSet-method show,ACMECalcSet-method threshold,ACMECalcSet-method vals,ACMECalcSet-method |
| Class "ACMESet" | ACMESet-class chromosome,ACMESet-method end,ACMESet-method plot,ACMESet-method start,ACMESet-method |
| Class for storing GFF-like data | aGFF-class plot,aGFF-method print,aGFF-method show,aGFF-method |
| Class "aGFFCalc" | aGFFCalc-class plot,aGFFCalc-method print,aGFFCalc-method show,aGFFCalc-method |
| Perform ACME calculation | do.aGFF.calc |
| An example ACME data structure of class ACMESet | example.agff |
| Find closest refseq gene | findClosestGene |
| Find all regions in data above p-value threshold | findRegions |
| Generics defined within ACME | chromosome cutpoints end plot start threshold vals |
| Get the refflat table from ucsc for the given genome | getRefflat |
| Read Nimblegen GFF files | read.resultsGFF |
| Write bedGraph format tracks for UCSC genome browser | write.bedGraph |
| Write Affy IGB .sgr format files | write.sgr |
