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l.zappia authored
* master: (175 commits) Fix comparison plots Bioconductor 3.5 release bump x.y.z versions to odd y after creation of 3_5 branch bump x.y.z versions to even y prior to creation of 3_5 branch Update NEWS and DESCRIPTION Version 0.99.15 Remove dropout.present estimation Add limits to zeros plots Adjust default splat DE fac params Add BPPARAM to scDDSimulate Add summariseDiff function Version 0.99.14 Add panel function to vignette Change var plot scale Run checks Update panel functions Add makeOverallPanel function Add makeDiffPanel function Add options to comparison plots Version 0.99.13 ... From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129246 bc3139a8-67e5-0310-9ffc-ced21a209358
l.zappia authored* master: (175 commits) Fix comparison plots Bioconductor 3.5 release bump x.y.z versions to odd y after creation of 3_5 branch bump x.y.z versions to even y prior to creation of 3_5 branch Update NEWS and DESCRIPTION Version 0.99.15 Remove dropout.present estimation Add limits to zeros plots Adjust default splat DE fac params Add BPPARAM to scDDSimulate Add summariseDiff function Version 0.99.14 Add panel function to vignette Change var plot scale Run checks Update panel functions Add makeOverallPanel function Add makeDiffPanel function Add options to comparison plots Version 0.99.13 ... From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129246 bc3139a8-67e5-0310-9ffc-ced21a209358
Splatter
Splatter is an R package for the simple simulation of single-cell RNA sequencing data. Splatter provides a common interface to multiple simulations that have:
- Functions for estimating simulation parameters
- Objects for storing those parameters
- Functions for simulating counts using those parameters
Splatter is built on top of scater and stores simulations in
SCESet objects. Splatter also has functions for comparing simulations and real
datasets.
Installation.
Development version
Splatter has been accepted into the latest version of Bioconductor and hence requires the latest version of R (>=3.4).
If you have these installed Splatter can be installed from Bioconductor using
biocLite:
source("https://bioconductor.org/biocLite.R")
biocLite("splatter")If you wish to build a local version of the vignette use:
biocLite("splatter", build_vignettes=TRUE)This will also build the vignette and install all suggested dependencies (which aren't required for core functionality). Building the vignette may sometimes fail when run from the command line, if this happens try running the install command in RStudio.
Getting started
Once installed the best place to get started is the vignette. For most users the most convient way to access this is online here.
Alternatively, if you chose to build the vignette, you can load Splatter, then browse the vignettes:
library(splatter)
browseVignettes("splatter")This is a detailed document that introduces the main features of Splatter.