Package: nempi 1.21.0

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]

nempi_1.21.0.tar.gz
nempi_1.21.0.zip(r-4.7)nempi_1.21.0.zip(r-4.6)nempi_1.21.0.zip(r-4.5)
nempi_1.21.0.tgz(r-4.6-any)nempi_1.21.0.tgz(r-4.5-any)
nempi_1.21.0.tar.gz(r-4.7-any)nempi_1.21.0.tar.gz(r-4.6-any)
nempi_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nempi/json (API)

# 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-1.21.0(bioc 3.24)nempi-1.20.0(bioc 3.23)

software geneexpression differentialexpression differentialmethylation genesignaling pathways network classification neuralnetwork networkinference atacseq dnaseq rnaseq pooledscreens crispr singlecell systemsbiology

4.60 score 2 stars 4 scripts 321 downloads 4 exports 99 dependencies

Last updated from:99206de282. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	176
linux-devel-x86_64	OK	302
source / vignettes	OK	265
linux-release-x86_64	OK	312
macos-release-arm64	OK	209
macos-oldrel-arm64	OK	125
windows-devel	OK	177
windows-release	OK	179
windows-oldrel	OK	201
wasm-release	OK	146

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 farver fastcluster fastICA flexclust flexmix fpc gdata generics 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 naturalsort nlme nnet pcalg permute pkgconfig png prabclus proxy R6 randomForest RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen Rgraphviz rlang robustbase Rtsne S7 scales sfsmisc snow snowfall statmod tsne vcd vctrs vegan viridisLite wesanderson withr XML zoo

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

Rendered fromnempi.Rmdusingknitr::rmarkdown

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