Package: nempi 1.13.0

Martin Pirkl

nempi: Inferring unobserved perturbations from gene expression data

Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.

Authors:Martin Pirkl [aut, cre]

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nempi.pdf |nempi.html✨
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NEWS

# Install 'nempi' in R:

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

Bug tracker:https://github.com/cbg-ethz/nempi/issues

On BioConductor:nempi-1.13.0(bioc 3.20)nempi-1.12.0(bioc 3.19)

bioconductor-package

4 exports 0.71 score 104 dependencies

Last updated 2 months agofrom:7e0620fd08

Exports:classpi nempi nempibs pifit

Dependencies:abind amap apcluster bdsmatrix BH BiocGenerics BiocManager BoolNet BoutrosLab.plotting.general class cli clue cluster colorspace corpcor cpp11 data.table deldir DEoptimR diptest e1071 ellipse epiNEM fansi farver fastcluster fastICA flexclust flexmix fpc gdata ggdendro ggm ggplot2 glue gmodels graph gridExtra gtable gtools hexbin igraph infotheo interp isoband jpeg kernlab labeling latex2exp lattice latticeExtra lifecycle limma Linnorm lmtest magrittr MASS Matrix matrixStats mclust mgcv minet mnem modeltools munsell naturalsort nlme nnet pcalg permute pillar pkgconfig png prabclus proxy R6 randomForest RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen Rgraphviz rlang robustbase Rtsne scales sfsmisc snow snowfall statmod stringi stringr tibble tsne utf8 vcd vctrs vegan viridisLite wesanderson withr XML zoo

| Nested Effects Models-based perturbation inference: | Inference of unobserved perturbations from gene expression profiles.

Martin Pirkl, Niko Beerenwinkel

Rendered fromnempi.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2022-09-23
Started: 2019-09-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Classification	classpi
Main function for NEM based perturbation imputation.	nempi
Bootstrapping function	nempibs
Accuracy computation	pifit
Plotting nempi	plot.nempi
Plot convergence of EM	plotConvergence.nempi