Package: netboost 2.15.0

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_2.15.0.tar.gz

netboost_2.15.0.tgz(r-4.4-x86_64)netboost_2.15.0.tgz(r-4.4-arm64)netboost_2.15.0.tgz(r-4.3-x86_64)netboost_2.15.0.tgz(r-4.3-arm64)
netboost_2.15.0.tar.gz(r-4.5-noble)netboost_2.15.0.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'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:netboost-2.15.0(bioc 3.21)netboost-2.14.0(bioc 3.20)

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

softwarestatisticalmethodgraphandnetworknetworkclusteringdimensionreductionbiomedicalinformaticsepigeneticsmetabolomicstranscriptomicscpp

4.18 score 1 scripts 136 downloads 12 exports 112 dependencies

Last updated 2 months agofrom:5fe0a608ec. Checks:OK: 1 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-linux-x86_64WARNINGNov 29 2024
R-4.4-mac-x86_64WARNINGNov 29 2024
R-4.4-mac-aarch64WARNINGNov 29 2024
R-4.3-mac-x86_64WARNINGNov 29 2024
R-4.3-mac-aarch64WARNINGNov 29 2024

Exports:cut_treesmcupgma_execnb_clustnb_distnb_filternb_mcupgmanb_moduleEigengenesnb_plot_dendronb_summarynb_transfernetboosttree_search

Dependencies:AnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiocManagerBiocStyleBiostringsbitbit64blobbookdownbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdigestdoParalleldynamicTreeCutevaluatefansifarverfastclusterfastmapfontawesomeforeachforeignFormulafsgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngpreprocessCoreR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppParallelrlangrmarkdownrpartRSQLiterstudioapiS4VectorssassscalesstringistringrsurvivalsystibbletinytexUCSC.utilsutf8vctrsviridisviridisLiteWGCNAwithrxfunXVectoryamlzlibbioc

The Netboost users guide

Pascal Schlosser, Jochen Knaus

Rendered fromnetboost.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
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 filtercalculate_adjacency
Function to calcutate distancecpp_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 stepcpp_filter_step
Tree search.cpp_tree_search
Module detection for an individual treecut_dendro
Module detection for the results from a nb_mcupgma callcut_trees
Execute a program/script from the installed MCUPGMA suite.mcupgma_exec
Netboost clustering stepnb_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 treetree_dendro
Extracts independent trees from nb_mcupgma results (external wrapper for internal C++ function)tree_search