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DESCRIPTION
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DESCRIPTION
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Package: GenomicBreaks
Type: Package
Title: Pairwise Alignment Breakpoint Analysis
Version: 0.14.7
Authors@R: c(
person("Charlotte", "West", email = "[email protected]", role = "aut"),
person("Charles", "Plessy", email = "[email protected]",
role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7410-6295")))
Description: Load pairwise genome alignments into objects, coalesce colinear
alignments to discover syntenic regions, flag inversions, and much more.
License: BSD_3_clause + file LICENSE
URL: https://oist.github.io/GenomicBreaks/,
https://github.com/oist/GenomicBreaks
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1),
GenomicRanges
Imports:
BiocGenerics,
BiocParallel,
CNEr,
genoPlotR,
ggplot2,
methods,
rtracklayer,
S4Vectors,
heatmaps,
IRanges,
GenomeInfoDb,
stats,
graphics,
Biostrings,
BSgenome,
Rcpp,
weights
LinkingTo: Rcpp
RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
Suggests:
BSgenome.Scerevisiae.UCSC.sacCer3,
GenomicFeatures,
gridExtra,
Gviz,
knitr,
plyranges,
rmarkdown
VignetteBuilder: knitr
Collate:
'GBreaksToMatrix.R'
'GOC.R'
'GenomicBreaks.R'
'RcppExports.R'
'StructuralVariants.R'
'dist2next.R'
'Translocations.R'
'align_scaf_plot_2.R'
'bp_coverage.R'
'bp_heatmap.R'
'bp_pair_analysis.R'
'bridgeRegions.R'
'chain_contigs.R'
'cleanGaps.R'
'zipWithNext.R'
'coalesce_contigs.R'
'correlation_index.R'
'feature_coverage.R'
'flagInversions.R'
'flagColinearAlignments.R'
'flagAll.R'
'flagLongShort.R'
'flagPairs.R'
'genoPlotR.R'
'getRefGenome.R'
'getSeq.R'
'get_bps.R'
'guessSeqLenghts.R'
'int_frag.R'
'inv2UCSCData.R'
'keepLongestPair.R'
'load_genomic_breaks.R'
'longestMatchesInTarget.R'
'makeInversions.R'
'makeOxfordPlots.R'
'mergeSeqLevels.R'
'orderQuerySeqLevels.R'
'pairwiseAlignment.R'
'reverse.R'
'scaf_align_plot.R'
'scaffoldByFlipAndMerge.R'
'serviceFunctions.R'
'splitSeqLevels.R'
'strandNames.R'
'strand_randomisation_index.R'
'swap.R'
'synteny_index.R'
'tan_bp.R'
'wholeGenomeClassification.R'