Package: RNAseqNet 0.1.5

Nathalie Vialaneix

RNAseqNet: Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation

Infer log-linear Poisson Graphical Model with an auxiliary data set. Hot-deck multiple imputation method is used to improve the reliability of the inference with an auxiliary dataset. Standard log-linear Poisson graphical model can also be used for the inference and the Stability Approach for Regularization Selection (StARS) is implemented to drive the selection of the regularization parameter. The method is fully described in <doi:10.1093/bioinformatics/btx819>.

Authors:Alyssa Imbert [aut], Nathalie Vialaneix [aut, cre]

RNAseqNet_0.1.5.tar.gz
RNAseqNet_0.1.5.tar.gz(r-4.7-any)RNAseqNet_0.1.5.tar.gz(r-4.6-any)
RNAseqNet_0.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RNAseqNet/json (API)

# Install 'RNAseqNet' in R:

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

Datasets:

lung - RNA-seq expression from lung tissue (GTEx).
thyroid - RNA-seq expression from thyroid tissue (GTEx).

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 10 scripts 308 downloads 8 exports 75 dependencies

Last updated from:8aa6fcb521. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	162
source / vignettes	OK	216
linux-release-x86_64	OK	166
wasm-release	OK	167

Exports:chooseSigma GLMnetToGraph GLMnetwork imputedGLMnetwork imputeHD RNAseqNetUsersGuide stabilitySelection varIntra

Dependencies:backports bit bit64 boot broom cli clipr codetools cpp11 crayon data.table dplyr farver forcats foreach generics ggplot2 glmnet glue gtable haven hms hot.deck igraph isoband iterators jomo labeling lattice lifecycle lme4 magrittr MASS Matrix mice minqa mitml nlme nloptr nnet numDeriv ordinal pan pillar pkgconfig PoiClaClu prettyunits progress purrr R6 rbibutils RColorBrewer Rcpp RcppEigen Rdpack readr reformulas rlang rpart S7 scales shape stringi stringr survival tibble tidyr tidyselect tzdb ucminf utf8 vctrs viridisLite vroom withr

Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation

Description | Reference | Session information for the vignette

Rendered fromRNAseqNet.Rmdusingknitr::rmarkdown

Last update: 2020-03-05
Started: 2017-05-16

Help page	Topics
Select the threshold sigma for hd-MI.	chooseSigma
Convert the result of imputedGLMnetwork or a matrix into a network.	GLMnetToGraph
Infer a network from RNA-seq expression.	GLMnetwork
Methods for 'GLMpath' objects.	GLMpath GLMpath-class print.GLMpath summary.GLMpath
Methods for 'HDImputed' objects.	HDImputed HDImputed-class print.HDImputed summary.HDImputed summary.HDimputed
Methods for 'HDpath' objects.	HDpath HDpath-class plot.HDpath print.HDpath summary.HDpath
Multiple hot-deck imputation and network inference from RNA-seq data.	imputedGLMnetwork
Impute missing row datasets with multiple hot deck.	imputeHD
RNA-seq expression from lung tissue (GTEx).	lung
View RNAseqNet User's Guide	RNAseqNetUsersGuide
Selection of the regularization parameter by StARS (Liu et al., 2010).	stabilitySelection
Methods for 'stars' objects.	plot.stars print.stars stars stars-class summary.stars
RNA-seq expression from thyroid tissue (GTEx).	thyroid
Average intra-donor pool variance.	varIntra

Package: RNAseqNet 0.1.5

RNAseqNet: Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation

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Help Manual

Usage by other packages (reverse dependencies)