destiny: Creates diffusion maps

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Create and plot diffusion maps.

Author
Philipp Angerer [cre, aut], Laleh Haghverdi [ctb], Maren Büttner [ctb], Fabian Theis [ctb], Carsten Marr [ctb], Florian Büttner [ctb]
Date of publication
None
Maintainer
Philipp Angerer <philipp.angerer@helmholtz-muenchen.de>
License
GPL
Version
2.0.2

View on Bioconductor

Man pages

coercions
Coercion methods
colorlegend
Color legend
cube_helix
Sequential color palette using the cube helix system
destiny
Create and plot diffusion maps
destiny-deprecated
Compatibility versions of functions for destiny 1.x scripts
destiny-generics
destiny generics
DiffusionMap-accessors
DiffusionMap accession methods
DiffusionMap-class
Create a diffusion map of cells
DiffusionMap-methods
DiffusionMap methods
dm_predict
Predict new data points using an existing DiffusionMap. The...
DPT
Diffusion Pseudo Time
DPT-matrix-methods
DPT Matrix methods
DPT-methods
DPT methods
eig_decomp
Fast eigen decomposition using ARPACK
ExpressionSet-helpers
Convert object to ExpressionSet or read it from a file
extractions
Extraction methods
find_dm_k
Find a suitable k
find_sigmas
Calculate the average dimensionality for m different gaussian...
find_tips
Find tips in a DiffusionMap object
guo
Guo at al. mouse embryonic stem cell qPCR data
l_which
Logical which
plot.DiffusionMap
3D or 2D plot of diffusion map
plot.DPT
Plot DPT
plot.Sigmas
Plot Sigmas object
random_root
Find a random root cell index
Sigmas-class
Sigmas Object
updateObject-method
Update old DiffusionMaps or Sigmas to a newer version

Files in this package

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