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:
RNAseqNet_0.1.5.tar.gz
RNAseqNet_0.1.5.tar.gz(r-4.5-noble)RNAseqNet_0.1.5.tar.gz(r-4.4-noble)
RNAseqNet_0.1.5.tgz(r-4.4-emscripten)RNAseqNet_0.1.5.tgz(r-4.3-emscripten)
RNAseqNet.pdf |RNAseqNet.html✨
RNAseqNet/json (API)
NEWS
| # Install 'RNAseqNet' in R: |
| install.packages('RNAseqNet', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 10 months agofrom:8aa6fcb521. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 17 2024 |
| R-4.5-linux | OK | Dec 17 2024 |
Exports:chooseSigmaGLMnetToGraphGLMnetworkimputedGLMnetworkimputeHDRNAseqNetUsersGuidestabilitySelectionvarIntra
Dependencies:backportsbitbit64bootbroomclicliprcodetoolscolorspacecpp11crayondata.tabledplyrfansifarverforcatsforeachgenericsggplot2glmnetgluegtablehavenhmshot.deckigraphisobanditeratorsjomolabelinglatticelifecyclelme4magrittrMASSMatrixmgcvmiceminqamitmlmunsellnlmenloptrnnetnumDerivordinalpanpillarpkgconfigPoiClaCluprettyunitsprogresspurrrR6RColorBrewerRcppRcppEigenreadrrlangrpartscalesshapestringistringrsurvivaltibbletidyrtidyselecttzdbucminfutf8vctrsviridisLitevroomwithr
Readme and manuals
Help Manual
| 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 |