Package: netboost 2.13.1

Pascal Schlosser

netboost: Network Analysis Supported by Boosting

Boosting supported network analysis for high-dimensional omics applications. This package comes bundled with the MC-UPGMA clustering package by Yaniv Loewenstein.

Authors:Pascal Schlosser [aut, cre], Jochen Knaus [aut, ctb], Yaniv Loewenstein [aut]

netboost_2.13.1.tar.gz

netboost_2.13.1.tgz(r-4.4-x86_64)netboost_2.13.1.tgz(r-4.3-x86_64)
netboost_2.13.1.tar.gz(r-4.5-noble)netboost_2.13.1.tar.gz(r-4.4-noble)
netboost.pdf |netboost.html✨
netboost/json (API)
NEWS

# Install 'netboost' in R:

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

tcga_aml_meth_rna_chr18 - TCGA RNA and methylation measurement on a subset of chromosome 18 for 80 AML patients.

On BioConductor:netboost-2.13.0(bioc 3.20)netboost-2.12.0(bioc 3.19)

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

bioconductor-package

12 exports 0.91 score 111 dependencies

Last updated 28 days agofrom:09d03ed721

Exports:cut_trees mcupgma_exec nb_clust nb_dist nb_filter nb_mcupgma nb_moduleEigengenes nb_plot_dendro nb_summary nb_transfer netboost tree_search

Dependencies:AnnotationDbi askpass backports base64enc Biobase BiocGenerics BiocManager BiocStyle Biostrings bit bit64 blob bookdown bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI digest doParallel dynamicTreeCut evaluate fansi farver fastcluster fastmap fontawesome foreach foreign Formula fs GenomeInfoDb GenomeInfoDbData ggplot2 glue GO.db gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png preprocessCore R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppParallel rlang rmarkdown rpart RSQLite rstudioapi S4Vectors sass scales stringi stringr survival sys tibble tinytex UCSC.utils utf8 vctrs viridis viridisLite WGCNA withr xfun XVector yaml zlibbioc

The Netboost users guide

Pascal Schlosser, Jochen Knaus

Rendered fromnetboost.Rmdusingknitr::rmarkdownon Jun 13 2024.

Last update: 2023-03-02
Started: 2019-03-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Package startup: used to fetch installation path of the own package, as required for executing binary programs delivered with it.	.onAttach
Calculate network adjacencies for filter	calculate_adjacency
Function to calcutate distance	cpp_dist_tom
Initialise boosting with chosen accelerator hardware (x86, AVX, FMA)	cpp_filter_base
Boosting cleanup (required to free memory)	cpp_filter_end
Single boosting step	cpp_filter_step
Tree search.	cpp_tree_search
Module detection for an individual tree	cut_dendro
Module detection for the results from a nb_mcupgma call	cut_trees
Execute a program/script from the installed MCUPGMA suite.	mcupgma_exec
Netboost clustering step	nb_clust
Calculate distance (external wrapper for internal C++ function) Parallelisation inside C++ program with RcppParallel.	nb_dist
Boosting via C++ function. Parallelisation by R-package parallel with forking (overhead of this method does not fall into account as single steps are ~10s).	nb_filter
Calculate dendrogram for a sparse distance matrix (external wrapper MC-UPGMA clustering package Loewenstein et al.	nb_mcupgma
Netboost module aggregate extraction.	nb_moduleEigengenes
Plot dendrogram from Netboost output.	nb_plot_dendro
Summarize results from a forest. Plot trees together.	nb_summary
Transfer of Netboost clustering to new data.	nb_transfer
Netboost clustering.	netboost
Returns the absolute path to folder with mcupgma executables and scripts.	netboostMCUPGMAPath
Returns the absolute path to "exec" folder in the package.	netboostPackagePath
Cleans the netboost temporary folder. This can be useful during the session as mcupgma creates vast directory structures (for iterations). Creates the own folder (all netboost temporary data is stored in netboostTmpPath(), which is equal to tempdir()/netboost). Also used for first time setup of folder.	netboostTmpCleanup
Returns the absolute path to temporary folder of the package. To change temporary path, use normal R variables (TEMPDIR etc).	netboostTmpPath
TCGA RNA and methylation measurement on a subset of chromosome 18 for 80 AML patients.	tcga_aml_meth_rna_chr18
Calculate the dendrogram for an individual tree	tree_dendro
Extracts independent trees from nb_mcupgma results (external wrapper for internal C++ function)	tree_search