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SingleCellAssay

Infrastructure and Tools for Single Cell Assay Analysis

Installation Instructions

 install.packages('devtools')
 library(devtools)
 install_github('SingleCellAssay', 'RGLab')
 vignette('SingleCellAssay-intro')

New Features

Hurdle Model implemented in zlm.SingleCellAssay
Thresholding support for NanoString in thresholdNanoString

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Version

Version

0.80

License

Artistic-2.0

Maintainer

Greg Finak

Last Published

December 22nd, 2017

Functions in SingleCellAssay (0.80)

Likelihood Ratio Tests for SingleCellAssays

NanoStringAssay

NanoString Assay Constructor

SingleCellAssay-package

"Tools for Single Cell Assay Analysis"

SingleCellAssay

SingleCellAssay: A constructor for an object of type SingleCellAssay.

RNASeqAssay-class

RNASeqAssay class. Doesn't require ncells

SCASet is a set of SingleCellAssay objects or objects of its subclasses (i.e. FluidigmAssay) The constructor SCASet should be used to make objects of this class.

DataLayer-class

DataLayer class

Constructor for a FluidigmAssay

SCASet constructor

SingleCellAssay-class

SingleCellAssay class

burdenOfFiltering

Burden of filtering

cData,SingleCellAssay-method

Get cellData data.frame

Return a deep copy of an object

Exponential average

try to guess form of LHT

Accessor for wellKey

Accessor for cellData AnnotatedDataFrame

combine,SCASet,missing-method

Combines a SCASet into a unified SingleCellAssay

Accessor for featureData AnnotatedDataFrame

Filter a SingleCellAssay

ThresholdedNanoString-class

Holds output and diagnostics from thresholdNanoString Not intended to be called by the user.

Add Another Layer

Report the mean et value for each gene

Get name of active layer

length,SCASet-method

Get the length of an SCASet

Read a section of a Nanostring RCC file

Do two objects conform in dimension and type?

Report the proportion of expression for each gene

Pooled Gene Frequency Estimation

melt.SingleCellAssay

plotSCAConcordance

Concordance plots of filtered single vs n-cell assays

sampleNames,SCASet-method

get the sample names in an SCASet

[,SCASet,ANY,ANY,ANY-method

Subset an SCASet to a smaller SCASet

[,SCASet-method

Subset an SCASet to a smaller SCASet

Run a zero-inflated regression

[,SingleCellAssay,ANY,ANY,ANY-method

Subset a SingleCellAssay

[,SingleCellAssay-method

Subset a SingleCellAssay

Which layer is active?

Set name of active layer

get the sample names in an SCASet

combine,SingleCellAssay,ANY-method

Combine a SingleCellAssay and a vector, data.frame or AnnotatedDataFrame

combine,SingleCellAssay,SingleCellAssay-method

Combine two SingleCellAssay or derived classes

computeEtFromCt

computeEtFromCt

Plot a likelihood ratio test object

zlm.SingleCellAssay

zlm.SingleCellAssay

Report number of expressing cells per gene

Plot NanoString log Counts vs cluster ID

split,DataLayer-method

Split a DataLayer correctly

Report standard deviation of et, for positive et for each gene

lapply,SCASet-method

Apply a function to each member of a SCASet

Set active layer

show,DataLayer-method

[,DataLayer,ANY,ANY,ANY-method

Subset a DataLayer

[,DataLayer-method

Subset a DataLayer

mergeWithKeyFile

Merge NanoString lanes with a key file

How many layers does a DataLayer have?

thresholdNanoString

Estimate thresholds for positive expression

Convert a pair of character names to a list that can be placed into a data.table

split,SingleCellAssay-method

Split into SCASet

[[<-,DataLayer-method

Replace a section of a DataLayer

subset,SingleCellAssay-method

Subset a SingleCellAssay by data in cellData

Likelihood ratio test for hurdle model

thresholdNanoString,NanoStringAssay-method

Estimate thresholds for positive expression

Vbeta Data Set, FluidigmAssay

readNanoStringLanes

RCC Nanostring Reader

[[,DataLayer-method

Extract from a DataLayer

[[,SCASet-method

Index into an SCASet object

Evaluate an expression (returning a logical vector in the context of x

summary,SingleCellAssay-method

Summarize expression parameters