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noise (version 1.0.1)

Estimation of Intrinsic and Extrinsic Noise from Single-Cell Data

Description

Functions to calculate estimates of intrinsic and extrinsic noise from the two-reporter single-cell experiment, as in Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186. Functions implement multiple estimators developed for unbiasedness or min Mean Squared Error (MSE) in Fu, A. Q. and Pachter, L. (2016). Estimating intrinsic and extrinsic noise from single-cell gene expression measurements. Statistical Applications in Genetics and Molecular Biology, 15(6), 447-471.

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Install

install.packages('noise')

Monthly Downloads

574

Version

1.0.1

License

GPL (>= 2)

Maintainer

Last Published

January 7th, 2021

Functions in noise (1.0.1)

noise-package

noise
computeNoiseForSubset

Select a random subset of data for noise estimation.
simulateSC

Simulate single-cell expression levels of two reporters
computeExtrinsicNoiseKnownCor

Compute estimates of the extrinsic noise using a known correlation in the min-MSE estimator.
computeExtrinsicNoise

Compute estimates of the extrinsic noise.
computeIntrinsicNoise

Compute estimates of the intrinsic noise.
elowitz_data

Expression of reporter genes in the D22 and M22 E. coli cells from Elowitz et al (2002).
yang_nl10

Expression of reporter genes in the NL010 E. coli cells from Yang et al (2014).