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now depends on GenomicRanges
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPQC@90271 bc3139a8-67e5-0310-9ffc-ced21a209358
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Rory Stark committed May 13, 2014
1 parent 7f71756 commit 985bca0
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6 changes: 3 additions & 3 deletions DESCRIPTION
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@@ -1,16 +1,16 @@
Package: ChIPQC
Type: Package
Title: Quality metrics for ChIPseq data
Version: 1.1.4
Version: 1.1.5
Date: 2014-05-12
Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark
Maintainer: Tom Carroll <tc.infomatics@gmail.com>, Rory Stark <rory.stark@cruk.cam.ac.uk>
Description: Quality metrics for ChIPseq data
biocViews: Sequencing, ChIPSeq, QualityControl, ReportWriting
License: GPL (>= 3)
LazyLoad: yes
Depends: R (>= 3.0.0), ggplot2, DiffBind
Imports: BiocGenerics (>= 0.8.0), Rsamtools (>= 1.14.2), GenomicRanges (>= 1.14.4),
Depends: R (>= 3.0.0), ggplot2, DiffBind, GenomicRanges
Imports: BiocGenerics (>= 0.8.0), Rsamtools (>= 1.14.2),
chipseq (>= 1.12.0), GenomicAlignments (>= 0.99.2),
gtools, BiocParallel, methods, IRanges, reshape2, Nozzle.R1, Biobase,grDevices, stats, utils
Suggests: BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene,
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7 changes: 1 addition & 6 deletions NAMESPACE
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@@ -1,4 +1,3 @@
importClassesFrom(GenomicRanges, GRanges, Seqinfo)

importClassesFrom(IRanges, DataFrame, IRanges, Rle)

Expand All @@ -13,9 +12,6 @@ importMethodsFrom(BiocParallel, bplapply)

importMethodsFrom(GenomicAlignments, readGAlignmentsFromBam)

importMethodsFrom(GenomicRanges, seqlengths, "seqlengths<-",
"seqlevels<-", seqnames)

importMethodsFrom(IRanges, "%in%", as.list, as.matrix, "colnames<-",
countOverlaps, coverage, elementMetadata,
"elementMetadata<-", end, flank, gsub, mean, median,
Expand All @@ -33,8 +29,7 @@ importFrom(Biobase, selectSome)

import(DiffBind)

importFrom(GenomicRanges, GIntervalTree, GRanges, GRangesList,
makeGRangesFromDataFrame)
import(GenomicRanges)

importFrom(ggplot2, aes, aes_string, element_blank, element_text,
facet_grid, facet_wrap, geom_bar, geom_boxplot, geom_line,
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