git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@95795 bc3139a8-67e5-0310-9ffc-ced21a209358
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Package: SplicingGraphs |
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Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads |
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to them |
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-Version: 1.7.0 |
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+Version: 1.7.1 |
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Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages |
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License: Artistic-2.0 |
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Description: This package allows the user to create, manipulate, and visualize |
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@@ -234,7 +234,7 @@ SplicingGraphs(x, grouping=NULL, min.ntx=2, max.ntx=NA, check.introns=TRUE) |
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library(GenomicFeatures) |
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suppressWarnings( |
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- toy_genes_txdb <- makeTranscriptDbFromGFF(toy_genes_gff()) |
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+ toy_genes_txdb <- makeTxDbFromGFF(toy_genes_gff()) |
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) |
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|
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## --------------------------------------------------------------------- |
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@@ -40,7 +40,7 @@ toy_overlaps() |
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\link[GenomicAlignments]{GAlignmentPairs} classes defined |
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in the \pkg{GenomicAlignments} package. |
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- \item The \code{\link[GenomicFeatures]{makeTranscriptDbFromGFF}} |
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+ \item The \code{\link[GenomicFeatures]{makeTxDbFromGFF}} |
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function and the \link[GenomicFeatures]{TxDb} class |
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defined in the \pkg{GenomicFeatures} package. |
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} |
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@@ -57,7 +57,7 @@ cat(readLines(toy_genes_gff()), sep="\n") |
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|
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library(GenomicFeatures) |
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suppressWarnings( |
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- txdb <- makeTranscriptDbFromGFF(toy_genes_gff()) |
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+ txdb <- makeTxDbFromGFF(toy_genes_gff()) |
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) |
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## Plot all the transcripts in the gene model: |