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  1. r3Cseq
  2. NAMESPACE
Browse code

r3Cseq 1.55.1: Replace GenomeInfoDb with Seqinfo

Hervé Pagès authored on 24/07/2025 23:32:26
Showing 1 changed files
NAMESPACE
History View file @ 87fafb1
... ... 
@@ -3,7 +3,7 @@ import(methods)
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 importMethodsFrom(Biostrings, reverseComplement, matchPattern,
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 	DNAString)
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-importMethodsFrom(GenomeInfoDb, seqlengths, "seqlengths<-",
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+importMethodsFrom(Seqinfo, seqlengths, "seqlengths<-",
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 	"seqlevels<-")
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 importFrom(RColorBrewer, brewer.pal)
Browse code

code clean up

- Move packages not useful to the end user to DESCRIPTION Imports:
- Adjust NAMESPACE to import necessary packages, functions, classes
- use full names for function arguments (e.g., axis(labels=...))


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/r3Cseq@97463 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 07/12/2014 23:25:24
Showing 1 changed files
NAMESPACE
History View file @ 26c9063
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@@ -1,6 +1,34 @@
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+import(methods)
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+
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+importMethodsFrom(Biostrings, reverseComplement, matchPattern,
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+	DNAString)
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+
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+importMethodsFrom(GenomeInfoDb, seqlengths, "seqlengths<-",
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+	"seqlevels<-")
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+
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+importFrom(RColorBrewer, brewer.pal)
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+
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+importFrom(Rsamtools, scanBamFlag)
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+importMethodsFrom(Rsamtools, scanBam, ScanBamParam)
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+
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+importFrom(VGAM, vsmooth.spline, zeta)
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+
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+importFrom(data.table, data.table, setkey, setnames)
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+
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+importFrom(qvalue, qvalue)
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+
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+importFrom(sqldf, sqldf)
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+
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+importFrom(stats, lm, pchisq, pnorm, smooth.spline)
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+
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+importFrom(utils, write.table)
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+
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+import(IRanges, GenomicRanges, rtracklayer)
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+
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 exportClasses(
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     "r3Cseq","r3CseqInBatch"
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 )
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+
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 export(
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     "getCoverage",
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     "expCoverage",
Browse code

This is r3Cseq version 1.5.0. This updated version provides more functionality to facilitate the analysis of 3C-seq data. For more details see the NEWS file.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/r3Cseq@71759 bc3139a8-67e5-0310-9ffc-ced21a209358

Supat Thongjuea authored on 10/12/2012 11:42:24
Showing 1 changed files
NAMESPACE
History View file @ d059853
... ... 
@@ -1,23 +1,41 @@
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 exportClasses(
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-    "r3Cseq"
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+    "r3Cseq","r3CseqInBatch"
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 )
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 export(
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     "getCoverage",
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     "expCoverage",
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     "contrCoverage",
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+    "getRawReads",
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+    "expRawData",
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+    "expRawData<-",
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+    "contrRawData",
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+    "contrRawData<-",
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+    "getBatchRawReads",
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     "getReadCountPerRestrictionFragment",
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+    "getBatchReadCountPerRestrictionFragment",
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+    "getReadCountPerWindow",
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+    "getBatchReadCountPerWindow",
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     "getViewpoint",
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     "calculateRPM",
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+    "calculateBatchRPM",
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+    "expReadCount",
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+    "contrReadCount",
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     "expRPM",
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     "contrRPM",
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     "getInteractions",
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+    "getBatchInteractions",
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     "expInteractionRegions",
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     "contrInteractionRegions",
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     "plotOverviewInteractions",
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     "plotInteractionsNearViewpoint",
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     "plotInteractionsPerChromosome",
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+    "plotDomainogramNearViewpoint",
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     "plot3Cecdf",
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+    "export3CseqRawReads2bedGraph",
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     "export3Cseq2bedGraph",
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     "exportInteractions2text",
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-    "generate3CseqReport"
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+    "exportBatchInteractions2text",
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+    "generate3CseqReport",
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+    "getExpInteractionsInRefseq",
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+    "getContrInteractionsInRefseq"
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 )
Browse code

per maintainer's request, replaced package with BioC 2.10 version, bumpped version to 1.3.1

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/r3Cseq@69624 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 20/09/2012 20:50:06
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NAMESPACE
History View file @ 92a6ade
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new file mode 100644
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@@ -0,0 +1,23 @@
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+exportClasses(
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+    "r3Cseq"
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+)
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+export(
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+    "getCoverage",
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+    "expCoverage",
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+    "contrCoverage",
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+    "getReadCountPerRestrictionFragment",
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+    "getViewpoint",
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+    "calculateRPM",
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+    "expRPM",
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+    "contrRPM",
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+    "getInteractions",
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+    "expInteractionRegions",
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+    "contrInteractionRegions",
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+    "plotOverviewInteractions",
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+    "plotInteractionsNearViewpoint",
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+    "plotInteractionsPerChromosome",
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+    "plot3Cecdf",
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+    "export3Cseq2bedGraph",
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+    "exportInteractions2text",
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+    "generate3CseqReport"
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+)
Browse code

preparing to replace package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/r3Cseq@69623 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 20/09/2012 20:47:07
Showing 1 changed files
NAMESPACE
History View file @ a8705e8
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deleted file mode 100644
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@@ -1,23 +0,0 @@
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-exportClasses(
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-    "r3Cseq"
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-)
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-export(
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-    "getCoverage",
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-    "expCoverage",
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-    "contrCoverage",
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-    "getReadCountPerRestrictionFragment",
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-    "getViewpoint",
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-    "calculateRPM",
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-    "expRPM",
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-    "contrRPM",
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-    "getInteractions",
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-    "expInteractionRegions",
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-    "contrInteractionRegions",
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-    "plotOverviewInteractions",
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-    "plotInteractionsNearViewpoint",
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-    "plotInteractionsPerChromosome",
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-    "plot3Cecdf",
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-    "export3Cseq2bedGraph",
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-    "exportInteractions2text",
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-    "generate3CseqReport"
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-)
Browse code

Adds r3Cseq to the repos.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/r3Cseq@59425 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 19/10/2011 16:32:03
Showing 1 changed files
NAMESPACE
History View file @ 6483657
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new file mode 100644
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@@ -0,0 +1,23 @@
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+exportClasses(
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+    "r3Cseq"
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+)
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+export(
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+    "getCoverage",
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+    "expCoverage",
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+    "contrCoverage",
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+    "getReadCountPerRestrictionFragment",
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+    "getViewpoint",
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+    "calculateRPM",
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+    "expRPM",
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+    "contrRPM",
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+    "getInteractions",
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+    "expInteractionRegions",
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+    "contrInteractionRegions",
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+    "plotOverviewInteractions",
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+    "plotInteractionsNearViewpoint",
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+    "plotInteractionsPerChromosome",
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+    "plot3Cecdf",
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+    "export3Cseq2bedGraph",
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+    "exportInteractions2text",
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+    "generate3CseqReport"
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+)