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DESCRIPTION
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DESCRIPTION
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Type: Package
Package: seqplots
Title: An interactive tool for visualizing NGS signals and sequence motif
densities along genomic features using average plots and heatmaps
Version: 1.23.3
Date: 2014-09-15
Authors@R:
person(given = "Przemyslaw",
family = "Stempor",
role = c("aut", "cph", "cre"),
email = "ps562@cam.ac.uk")
Maintainer: Przemyslaw Stempor <ps562@cam.ac.uk>
Description: SeqPlots is a tool for plotting next generation sequencing
(NGS) based experiments' signal tracks, e.g. reads coverage from
ChIP-seq, RNA-seq and DNA accessibility assays like DNase-seq and
MNase-seq, over user specified genomic features, e.g. promoters, gene
bodies, etc. It can also calculate sequence motif density profiles
from reference genome. The data are visualized as average signal
profile plot, with error estimates (standard error and 95% confidence
interval) shown as fields, or as series of heatmaps that can be sorted
and clustered using hierarchical clustering, k-means algorithm and
self organising maps. Plots can be prepared using R programming
language or web browser based graphical user interface (GUI)
implemented using Shiny framework. The dual-purpose implementation
allows running the software locally on desktop or deploying it on
server. SeqPlots is useful for both for exploratory data analyses and
preparing replicable, publication quality plots. Other features of the
software include collaboration and data sharing capabilities, as well
as ability to store pre-calculated result matrixes, that combine many
sequencing experiments and in-silico generated tracks with multiple
different features. These binaries can be further used to generate new
combination plots on fly, run automated batch operations or share with
colleagues, who can adjust their plotting parameters without loading
actual tracks and recalculating numeric values. SeqPlots relays on
Bioconductor packages, mainly on rtracklayer for data input and
BSgenome packages for reference genome sequence and annotations.
License: GPL-3
URL: http://github.com/przemol/seqplots
BugReports: http://github.com/przemol/seqplots/issues
Depends:
R (>= 3.2.0)
Imports:
methods,
IRanges,
BSgenome,
digest,
rtracklayer,
GenomicRanges,
Biostrings,
shiny (>= 0.13.0),
DBI,
RSQLite,
plotrix,
fields,
grid,
kohonen,
parallel,
GenomeInfoDb,
class,
S4Vectors,
ggplot2,
reshape2,
gridExtra,
jsonlite,
DT (>= 0.1.0),
RColorBrewer,
Rsamtools,
GenomicAlignments,
BiocManager
Suggests:
testthat,
BiocStyle,
knitr,
rmarkdown,
covr
VignetteBuilder: knitr
biocViews: ImmunoOncology, ChIPSeq, RNASeq, Sequencing, Software, Visualization
LazyLoad: yes
RoxygenNote: 6.1.1
Collate:
'MotifSetup-class.R'
'PlotSetPair-class.R'
'PlotSetArray-class.R'
'PlotSetList-class.R'
'add_local_files.R'
'deployServerInstance.R'
'generic_methods.R'
'getPlotSetArray.R'
'helper_functions.R'
'int_getSF.R'
'int_ggHeatmapPlotWrapper.R'
'int_heatmapPlotWrapper.R'
'int_imPlot2.R'
'int_plotMext.R'
'plotAverage.R'
'plotHeatmap.R'
'run.R'
'seqplots-package.R'
'zzz.R'