destiny: Creates diffusion maps

Create and plot diffusion maps.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("destiny")
AuthorPhilipp Angerer [cre, aut], Laleh Haghverdi [ctb], Maren Büttner [ctb], Fabian Theis [ctb], Carsten Marr [ctb], Florian Büttner [ctb]
Bioconductor views CellBasedAssays CellBiology Clustering Software Visualization
Date of publicationNone
MaintainerPhilipp Angerer <philipp.angerer@helmholtz-muenchen.de>
LicenseGPL
Version2.0.8

View on Bioconductor

Functions

as.data.frame.DiffusionMap Man page
as.data.frame,DiffusionMap-method Man page
as.data.frame.DPT Man page
as.data.frame,DPT-method Man page
as.ExpressionSet Man page
as.ExpressionSet,data.frame-method Man page
as.ExpressionSet-method Man page
as.matrix.DPT Man page
as.matrix,DPT-method Man page
branch_divide Man page
coercions Man page
colorlegend Man page
cube_helix Man page
cube.helix Man page
data:guo Man page
data:guo_norm Man page
dataset Man page
dataset<- Man page
dataset<-,DiffusionMap-method Man page
dataset,DiffusionMap-method Man page
dataset<-,DPT-method Man page
dataset,DPT-method Man page
destiny Man page
destiny-deprecated Man page
destiny generics Man page
destiny-package Man page
DiffusionMap Man page
DiffusionMap accessors Man page
[[,DiffusionMap,character,missing-method Man page
DiffusionMap class Man page
DiffusionMap-class Man page
DiffusionMapCompat Man page
$,DiffusionMap-method Man page
DiffusionMap methods Man page
DiffusionMap-methods Man page
dim.DPT Man page
distance Man page
distance<- Man page
distance<-,DiffusionMap-method Man page
distance,DiffusionMap-method Man page
dm_predict Man page
dm.predict Man page
DPT Man page
[.DPT Man page
[[,DPT,character,missing-method Man page
DPT-class Man page
DPT matrix methods Man page
$,DPT-method Man page
DPT methods Man page
eig_decomp Man page
eig.decomp Man page
eigenvalues Man page
eigenvalues<- Man page
eigenvalues<-,DiffusionMap-method Man page
eigenvalues,DiffusionMap-method Man page
eigenvectors Man page
eigenvectors<- Man page
eigenvectors<-,DiffusionMap-method Man page
eigenvectors,DiffusionMap-method Man page
ExpressionSet helpers Man page
extractions Man page
find_dm_k Man page
find.dm.k Man page
find_sigmas Man page
find.sigmas Man page
find_tips Man page
fortify.DiffusionMap Man page
fortify.DPT Man page
guo Man page
guo_norm Man page
l_which Man page
lWhich Man page
names.DiffusionMap Man page
names,DiffusionMap-method Man page
names.DPT Man page
names,DPT-method Man page
ncol.DPT Man page
nrow.DPT Man page
optimal_sigma Man page
optimal.sigma Man page
optimal_sigma,DiffusionMap-method Man page
optimal_sigma,Sigmas-method Man page
plot.DiffusionMap Man page
plot,DiffusionMap,missing-method Man page
plot,DiffusionMap,numeric-method Man page
plot.DPT Man page
plot,DPT,missing-method Man page
plot,DPT,numeric-method Man page
plot.Sigmas Man page
plot,Sigmas,missing-method Man page
print.DiffusionMap Man page
print,DiffusionMap-method Man page
print,Sigmas-method Man page
random_root Man page
read.ExpressionSet Man page
scale_color_cube_helix Man page
scale_colour_cube_helix Man page
scale_fill_cube_helix Man page
show.DiffusionMap Man page
show,DiffusionMap-method Man page
show,Sigmas-method Man page
sigmas Man page
sigmas<- Man page
Sigmas Man page
Sigmas class Man page
Sigmas-class Man page
sigmas<-,DiffusionMap-method Man page
sigmas,DiffusionMap-method Man page
Sigmas-methods Man page
tips Man page
updateObject,DiffusionMap-method Man page
updateObject-method Man page
updateObject,Sigmas-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R R/aaa.r R/accessor-generics.r R/censoring.r R/colorlegend.r R/compat.r R/cube_helix.r R/destiny-package.r R/diffusionmap-methods-accession.r R/diffusionmap-methods.r R/diffusionmap-plotting.r R/diffusionmap.r R/dist-matrix-coerce.r R/dpt-branching.r R/dpt-helpers.r R/dpt-methods-matrix.r R/dpt-methods.r R/dpt-plotting.r R/dpt.r R/eig_decomp.r R/expressionset-helpers.r R/find_dm_k.r R/guo-data.r R/l_which.r R/methods-coercion.r R/methods-extraction.r R/methods-update.r R/plothelpers.r R/predict.r R/s4-unions.r R/sigmas-plotting.r R/sigmas.r R/utils.r
build
build/vignette.rds
data
data/guo.rda
data/guo_norm.rda
demo
demo/00Index
demo/destiny.r
inst
inst/CITATION
inst/doc
inst/doc/DPT.ipynbmeta
inst/doc/DPT.pdf
inst/doc/DPT.r
inst/doc/Diffusion-Map-recap.ipynbmeta
inst/doc/Diffusion-Map-recap.pdf
inst/doc/Diffusion-Map-recap.r
inst/doc/Diffusion-Maps.ipynbmeta
inst/doc/Diffusion-Maps.pdf
inst/doc/Diffusion-Maps.r
inst/doc/Global-Sigma.ipynbmeta
inst/doc/Global-Sigma.pdf
inst/doc/Global-Sigma.r
man
man/DPT-matrix-methods.Rd man/DPT-methods.Rd man/DPT.Rd man/DiffusionMap-accessors.Rd man/DiffusionMap-class.Rd man/DiffusionMap-methods.Rd man/ExpressionSet-helpers.Rd man/Sigmas-class.Rd man/coercions.Rd man/colorlegend.Rd man/cube_helix.Rd man/destiny-deprecated.Rd man/destiny-generics.Rd man/destiny.Rd man/dm_predict.Rd man/eig_decomp.Rd man/extractions.Rd man/find_dm_k.Rd man/find_sigmas.Rd man/find_tips.Rd man/guo.Rd man/l_which.Rd man/plot.DPT.Rd man/plot.DiffusionMap.Rd man/plot.Sigmas.Rd man/random_root.Rd man/updateObject-method.Rd
src
src/Makevars
src/RcppExports.cpp
src/censoring.cpp
src/no_censoring.cpp
vignettes
vignettes/DPT.ipynb
vignettes/DPT.ipynbmeta
vignettes/Diffusion-Map-recap.ipynb
vignettes/Diffusion-Map-recap.ipynbmeta
vignettes/Diffusion-Maps.ipynb
vignettes/Diffusion-Maps.ipynbmeta
vignettes/Global-Sigma.ipynb
vignettes/Global-Sigma.ipynbmeta
vignettes/bibliography.bib
vignettes/destiny-base.tplx
vignettes/destiny-bib.tplx
vignettes/destiny.tplx
vignettes/destiny_processors.py
vignettes/mmc4.xls
vignettes/mmc6.xls

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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