evaluate.heterogeneity
function.evaluate.heterogeneity
function.incucyte
function.DE.status
functionplot.NES
plot.gsea
and plot.multi.gsea
volcano
to do not drop color levelsincucyte
functionplot.multi.gsea
, plot.NES
evaluate.heterogeneity
functionsvolcano
function in order to reduce the plot size for publicationsevaluate.heterogeneity
to enable the log1p signal in the heatmap and avoid scientific annotation of the rank numbersevaluate.heterogeneity
plot.gsea
enrichplot
and RColorBrewer
required for plot.gsea
evaluate.heterogeneity
, incucyte
, read.computeMatrix.file
, intersect.regions
, venn.overlap
and closest.regions
pkg.version
floating.floor
and floating.ceiling
plot.density.differences
, plot.density.profile
, plot.density.profile.smooth
and plot.density.summary
sort.bed
usage: a) removed redundant "export.bed" option (now it is sufficient to add a file name in the "export.file.name" parameter if exporting is wished), b) added the "unique.regions" option, c) minor bug fixed in sort.bed
for input class checksort.bed
and collapse.bed
functionsintersect.bed
and computeMatrix.deeptools
functionsdensity.matrix
density.matrix
density.matrix
, allowing the possibility to reverse the signal of strand '-' regionsdensity.matrix
get.single.base.score.bw
plot.density.profile.smooth
genomic.tracks
qPCR.rna.exp
qPCR.results
examplegenomic.tracks
and qPCR.rna.exp
requirements: colorspace, ggbio, ggforce, GenomicRanges, AnnotationFilter, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, openssl, readxl, jpegggpmisc
, prettydoc
, knitr
, rmarkdown
, stats
)density.matrix
(alternative to computeMatrix.deeptools
)RNAseq
, deeptools.matrix
, CNV.table
plot.density.differences
actualize
function to build vignettes and bugs fixedplot.density.summary
and plot.density.profile
functions in order to not interfer with other packagesplot.density.summary
and plot.density.profile
functions in order to keep the input order of the samples and groups in the plots colors/legendplot.density.profile
to change legend title when 'plot.by.group==FALSE'plot.density.summary
to compute the means comparisons even when not required to show on the plot and indicate whether the statistical test performed was paired or notplot.density.summary
functionpkg.version
outputggpubr
and removed labeling
actualize
and uniform.x.axis
functionsuniform.x.axis
and uniform.y.axis
plot.density.summary
and plot.density.profile
plot.density.summary
functionplot.density.summary
plot.density.summary
function a density profile corresponding to the summary plot subset range is generatedplot.density.summary
now contains also the orignal positions used to generate the matrixIGVsnap
function and improvment of relative manual informationIGVsnap
allows the addiction of a delay time between snap generationactualize
and integrated in each function to check everytime if Rseb
package is up-to-dateplot.density.summary
, floating.ceiling
, floating.floor
rvcheck
and curl
plot.density.profile
functionuniform.x.axis
and uniform.y.axis
with the new functions floating.ceiling
and floating.floor
and to support a given number of digitsDE.status
now supports also NAs for the FoldChangecolor.gradient
and is.color
volcano
plot.density.profile
build.bed
intersect.bedtools
labeling
)uniform.x.axis
and uniform.y.axis
volcano
function: parameter 'font_size' addedcomputeMatrix.deeptools
build.bed
dplyr
IGVsnap
functionpkg.check
read.computeMatrix.file
plot.density.profile
to be compatibile with outputs from read.computeMatrix.file
First release.
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