Package: MPRAnalyze 1.31.0

Tal Ashuach

MPRAnalyze: Statistical Analysis of MPRA data

MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes.

Authors:Tal Ashuach [aut, cre], David S Fischer [aut], Anat Kriemer [ctb], Fabian J Theis [ctb], Nir Yosef [ctb],

MPRAnalyze_1.31.0.tar.gz
MPRAnalyze_1.31.0.zip(r-4.7)MPRAnalyze_1.31.0.zip(r-4.6)MPRAnalyze_1.31.0.zip(r-4.5)
MPRAnalyze_1.31.0.tgz(r-4.6-any)MPRAnalyze_1.31.0.tgz(r-4.5-any)
MPRAnalyze_1.31.0.tar.gz(r-4.7-any)MPRAnalyze_1.31.0.tar.gz(r-4.6-any)
MPRAnalyze_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MPRAnalyze/json (API)

# Install 'MPRAnalyze' in R:

install.packages('MPRAnalyze', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yoseflab/mpranalyze/issues

Datasets:

ce.colAnnot - Sample MPRA data
ce.control - Sample MPRA data
ce.dnaCounts - Sample MPRA data
ce.rnaCounts - Sample MPRA data

On BioConductor:MPRAnalyze-1.31.0(bioc 3.24)MPRAnalyze-1.30.0(bioc 3.23)

immunooncology software statisticalmethod sequencing geneexpression cellbiology cellbasedassays differentialexpression experimentaldesign classification

7.04 score 13 stars 42 scripts 5 mentions 26 exports 37 dependencies

Last updated from:cd479d72ee. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	177
linux-devel-x86_64	OK	308
source / vignettes	OK	250
linux-release-x86_64	OK	290
macos-release-arm64	OK	143
macos-oldrel-arm64	OK	200
windows-devel	OK	210
windows-release	OK	216
windows-oldrel	OK	205
wasm-release	OK	126

Exports:analyzeComparative analyzeQuantification controls dnaAnnot dnaCounts dnaDepth estimateDepthFactors getAlpha getDistrParam_DNA getDistrParam_RNA getFits_DNA getFits_RNA getModelParameters_DNA getModelParameters_RNA model MpraObject rnaAnnot rnaCounts rnaDepth rowAnnot setDepthFactors setModel simulateMPRA testCoefficient testEmpirical testLrt

Dependencies:abind BH Biobase BiocGenerics BiocParallel cli codetools cpp11 crayon DelayedArray formatR futile.logger futile.options generics GenomicRanges glue hms IRanges lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats pkgconfig prettyunits progress R6 rlang S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment vctrs XVector

Analyzing MPRA data with MPRAnalyze

Rendered fromvignette.Rmdusingknitr::rmarkdown

Last update: 2020-08-21
Started: 2018-05-13

Help page	Topics
Run a comparative analysis between conditions	analyzeComparative
Perform quantitative analysis on the MPRA data. This analysis aims to determine which sequences have a regulatory function, when no condition is being tested.	analyzeQuantification
Sample MPRA data	ce.colAnnot ce.control ce.dnaCounts ce.rnaCounts ChrEpi
estimate library size correction factors	estimateDepthFactors
return the fitted value for the transcription rate.	getAlpha
Get model distribution parameters from an MpraObject of a given candidate enhancer	getDistrParam_DNA getDistrParam_RNA
Get DNA model-based estimates from an MpraObject (the expected values based on the model). These can be compared with the observed counts to assess goodness of fit.	getFits_DNA
Get RNA model-based estimates from an MpraObject (the expected values based on the model). These can be compared with the observed counts to assess goodness of fit.	getFits_RNA
extract the DNA model parameters	extractModelParameters_DNA extractModelParameters_RNA getModelParameters_DNA getModelParameters_RNA
MpraObject	controls controls,MpraObject-method dnaAnnot dnaAnnot,MpraObject-method dnaCounts dnaCounts,MpraObject-method dnaDepth dnaDepth,MpraObject-method model model,MpraObject-method MpraObject MpraObject,matrix-method MpraObject,SummarizedExperiment-method rnaAnnot rnaAnnot,MpraObject-method rnaCounts rnaCounts,MpraObject-method rnaDepth rnaDepth,MpraObject-method rowAnnot rowAnnot,MpraObject-method
Manually set library depth correction factors	setDepthFactors
Set the distributional model used. Default is gamma.pois, and is recommended. Other supoprted models are ln.nb in which the DNA follows a log-normal distribution and the RNA follows a negative binomial, and ln.ln in which both follow log-normal distributions. To use alternative distributional models, use this function before fitting the model.	setModel
Simulate an MPRA dataset	simulateMPRA
Calculate the significance of a factor in the regression model	testCoefficient
test for significant activity (quantitative analysis) using various empirical tests (see details)	testEmpirical
Calculate likelihood ratio test for the specific nested model	testLrt

Package: MPRAnalyze 1.31.0

MPRAnalyze: Statistical Analysis of MPRA data

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