Package: altcdfenvs 2.69.0
Laurent Gautier
altcdfenvs: alternative CDF environments (aka probeset mappings)
Convenience data structures and functions to handle cdfenvs
Authors:
altcdfenvs_2.69.0.tar.gz
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altcdfenvs.pdf |altcdfenvs.html✨
altcdfenvs/json (API)
| # Install 'altcdfenvs' in R: |
| install.packages('altcdfenvs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- cdfenvEx - CdfEnvAffy
On BioConductor:altcdfenvs-2.69.0(bioc 3.21)altcdfenvs-2.68.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarrayonechannelqualitycontrolpreprocessingannotationproprietaryplatformstranscription
Last updated 2 months agofrom:6869520f2f. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 27 2024 |
| R-4.5-win | NOTE | Nov 27 2024 |
| R-4.5-linux | NOTE | Dec 27 2024 |
| R-4.4-win | NOTE | Nov 27 2024 |
| R-4.4-mac | NOTE | Dec 27 2024 |
| R-4.3-win | NOTE | Nov 27 2024 |
| R-4.3-mac | NOTE | Dec 27 2024 |
Exports:appendCdfEnvAffybuildCdfEnv.biostringsbuildCdfEnv.matchprobescopyCdfEnvAffycountduplicatedcountskip.FASTA.entriesgeneNames.CdfEnvAffygetCdfEnvAffygetxy.probeseqgrep.FASTA.entryindex2xyindex2xy.CdfEnvAffyindexProbes.CdfEnvAffymatchAffyProbesmmProbesplot.CdfEnvAffyprint.FASTAprintValidCdfEnvAffyread.FASTA.entryread.n.FASTA.entriesread.n.FASTA.entries.splitread.n.FASTA.headersread.n.FASTA.sequencesremoveIndexskip.FASTA.entrytoHypergraphunique.CdfEnvAffyvalidAffyBatchvalidCdfEnvAffywrapCdfEnvAffywrite.FASTAxy2indexxy2index.CdfEnvAffy
Dependencies:affyaffyioaskpassBiobaseBiocGenericsBiocManagerBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatagraphhttrhypergraphIRangesjsonlitemakecdfenvmimeopensslpreprocessCoreR6S4VectorssysUCSC.utilsXVectorzlibbioc
altcdfenvs
Rendered fromaltcdfenvs.Rnwusingutils::Sweaveon Dec 27 2024.Last update: 2013-11-01
Started: 2013-11-01
Alternative CDF environments for 2(or more)-genomes chips
Rendered fromngenomeschips.Rnwusingutils::Sweaveon Dec 27 2024.Last update: 2019-02-25
Started: 2013-11-01
Modifying existing CDF environments to make alternative CDF environments
Rendered frommodify.Rnwusingutils::Sweaveon Dec 27 2024.Last update: 2019-02-25
Started: 2013-11-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class "AffyProbesMatch" | AffyProbesMatch-class combine,AffyProbesMatch,AffyProbesMatch-method show,AffyProbesMatch-method toHypergraph,AffyProbesMatch-method |
| append probe sets to a CdfEnvAffy | appendCdfEnvAffy |
| Build CDF environments | buildCdfEnv.biostrings |
| Class "CdfEnvAffy" | CdfEnvAffy-class coerce,CdfEnvAffy,Cdf-method coerce,CdfEnvAffy,environment-method geneNames,CdfEnvAffy-method index2xy,CdfEnvAffy-method indexProbes,CdfEnvAffy,character-method plot,CdfEnvAffy,missing-method show,CdfEnvAffy-method toHypergraph,CdfEnvAffy-method xy2index,CdfEnvAffy-method [,CdfEnvAffy,character,missing,missing-method |
| CdfEnvAffy | cdfenvEx |
| functions related to cdfenvs | buildCdfEnv.matchprobes CdfEnv getCdfEnvAffy wrapCdfEnvAffy |
| make a copy of a CdfEnvAffy | copyCdfEnvAffy |
| Count the number of times probes are used | countduplicated |
| get the names of the known probe sets | geneNames.CdfEnvAffy |
| A function to get the XY coordinates from a probes sequences data frame | getxy.probeseq |
| Functions to shuttle from indexes to XY coordinates | index2xy index2xy.CdfEnvAffy xy2index xy2index.CdfEnvAffy |
| indexes for probes | indexProbes.CdfEnvAffy |
| Match the probes on an Affymetrix array | matchAffyProbes mmProbes |
| A function to `plot' a CdfEnvAffy | plot.CdfEnvAffy |
| Functions to work with FASTA files / connections | countskip.FASTA.entries grep.FASTA.entry print.FASTA read.FASTA.entry read.n.FASTA.entries read.n.FASTA.entries.split read.n.FASTA.headers read.n.FASTA.sequences skip.FASTA.entry write.FASTA |
| A function to remove probes in an environment | removeIndex |
| Transform to an hypergraph | toHypergraph |
| Remove duplicated elements from a CdfEnvAffy | unique.CdfEnvAffy |
| Check validity of a CdfEnvAffy. | printValidCdfEnvAffy validAffyBatch validCdfEnvAffy |
