Browse code

Update version 1.9.1

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@128664 bc3139a8-67e5-0310-9ffc-ced21a209358

Wolfgang Kaisers authored on 13/04/2017 16:00:27
Showing1 changed files
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@@ -2,8 +2,11 @@
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 useDynLib(seqTools)
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 import(methods)
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 import(zlibbioc)
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-importFrom(utils,head)
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-importFrom(utils,tail)
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+importFrom(utils,"head", "tail")
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+importFrom("grDevices", "topo.colors")
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+importFrom("graphics", "axis", "legend", "lines", "plot")
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+importFrom("stats", "as.dist", "hclust")
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+
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 export(
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     ascii2char,
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     countDnaKmers,
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@@ -34,9 +37,11 @@ exportMethods(
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     collectDur,
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     gcContent,
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     gcContentMatrix,
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+    getGCcontent,
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     fileNames,
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     getK,
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     kmerCount,
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+    kmerSvd,
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     maxSeqLen,
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     meltDownK,
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     mergedPhred,
Browse code

add seqTools package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@95415 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 13/10/2014 19:02:34
Showing1 changed files
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new file mode 100644
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@@ -0,0 +1,65 @@
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+#exportPattern("^[[:alpha:]]+")
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+useDynLib(seqTools)
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+import(methods)
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+import(zlibbioc)
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+importFrom(utils,head)
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+importFrom(utils,tail)
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+export(
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+    ascii2char,
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+    countDnaKmers,
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+    countFastaKmers,
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+    countGenomeKmers,
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+    countSpliceKmers,
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+    char2ascii,
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+    kMerIndex,
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+    phredTable,
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+    fastqq,
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+    fastqKmerLocs,
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+    fastqKmerSubsetLocs,
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+    phredDist,
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+    plotPhredDist,
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+    plotPhredQuant,
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+    phredQuantiles,
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+    revCountDnaKmers,
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+    simFastqqRunTimes,
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+    sim_fq,
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+    trimFastq,
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+    writeFai,
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+    writeSimFastq,
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+    writeSimContFastq
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+)
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+exportMethods(
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+    cbDistMatrix,
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+    collectTime,
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+    collectDur,
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+    gcContent,
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+    gcContentMatrix,
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+    fileNames,
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+    getK,
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+    kmerCount,
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+    maxSeqLen,
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+    meltDownK,
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+    mergedPhred,
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+    mergedPhredQuantiles,
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+    mergeFastqq,
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+    nFiles,
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+    nNnucs,
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+    nReads,
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+    nucFreq,
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+    phred,
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+    plotGCcontent,
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+    plotKmerCount,
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+    plotMergedPhredQuant,
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+    plotNucCount,
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+    plotNucFreq,
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+    probeLabel,
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+    "probeLabel<-",
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+    propPhred,
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+    seqLen,
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+    seqLenCount
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+)
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+exportClasses(
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+    Fastqq
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+)
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+
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+