Package: DDPNA 0.3.0

DDPNA: Disease-Drived Differential Proteins Co-Expression Network Analysis

Functions designed to connect disease-related differential proteins and co-expression network. It provides the basic statics analysis included t test, ANOVA analysis. The network construction is not offered by the package, you can used 'WGCNA' package which you can learn in Peter et al. (2008) <doi:10.1186/1471-2105-9-559>. It also provides module analysis included PCA analysis, two enrichment analysis, Planner maximally filtered graph extraction and hub analysis.

Authors:Kefu Liu [aut, cre]

DDPNA_0.3.0.tar.gz
DDPNA_0.3.0.zip(r-4.5)DDPNA_0.3.0.zip(r-4.4)DDPNA_0.3.0.zip(r-4.3)
DDPNA_0.3.0.tgz(r-4.4-any)DDPNA_0.3.0.tgz(r-4.3-any)
DDPNA_0.3.0.tar.gz(r-4.5-noble)DDPNA_0.3.0.tar.gz(r-4.4-noble)
DDPNA_0.3.0.tgz(r-4.4-emscripten)DDPNA_0.3.0.tgz(r-4.3-emscripten)
DDPNA.pdf |DDPNA.html✨
DDPNA/json (API)

# Install 'DDPNA' in R:

install.packages('DDPNA', repos = c('https://liukf10.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/liukf10/ddpna/issues

Datasets:

On CRAN:

3.00 score 2 stars 4 scripts 251 downloads 25 exports 124 dependencies

Last updated 3 years agofrom:6ba3e7f936. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 09 2024
R-4.5-win	NOTE	Nov 09 2024
R-4.5-linux	NOTE	Nov 09 2024
R-4.4-win	NOTE	Nov 09 2024
R-4.4-mac	NOTE	Nov 09 2024
R-4.3-win	NOTE	Nov 09 2024
R-4.3-mac	NOTE	Nov 09 2024

Exports:anova_p changedID Data_impute dataStatInf DEP_Mod_HeatMap DEP_Mod_net_plot DEPsets fc.pos FCSenrichplot getmoduleHub groupmean ID_match MaxQdataconvert MaxQprotein ME_inf modpcomp Module_Enrich Module_inf moduleID multi.t.test P.G.extract rename_dupnewID single_mod_enrichplot SoftThresholdScaleGraph wgcnatest

Dependencies:ash askpass backports base64enc BH bslib cachem checkmate class cli cluster codetools colorspace cpp11 crosstalk curl data.table DEoptimR digest diptest doParallel dplyr evaluate extrafont extrafontdb fansi farver fastmap flexmix fontawesome foreach foreign formatR Formula fpc fs futile.logger futile.options generics ggalt ggforce ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr igraph isoband iterators jquerylib jsonlite kernlab KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle magrittr maps MASS Matrix mclust MEGENA memoise mgcv mime modeltools munsell nlme nnet openssl pillar pkgconfig plotly plyr polyclip prabclus proj4 promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape rlang rmarkdown robustbase rpart rstudioapi Rttf2pt1 sass scales stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tinytex tweenr utf8 vctrs VennDiagram viridis viridisLite withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Disease-drived Differential Proteins And Proteomic Co-expression Network Associated Analysis	DDPNA-package DDPNA
anova_p	anova_p
changedID	changedID
Data_impute	Data_impute
dataStatInf	dataStatInf
DEP_Mod_HeatMap	DEP_Mod_HeatMap
DEP_Mod_net_plot	DEP_Mod_net_plot
DEPsets	DEPsets
fc.pos	fc.pos
FCSenrichplot	FCSenrichplot
getmoduleHub	getmoduleHub
groupmean	groupmean
homolog protein Uniprot ID transformation	ID_match
one-step to extract 'Maxquant' quantification data and convert	MaxQdataconvert
read proteomic quantification data and seperate the protein information and quantification information.	MaxQprotein
module eigengenes information	ME_inf
modpcomp	modpcomp
Module_Enrich	Module_Enrich
Module and protein information.	Module_inf
extract intersection ID between dataset and module	moduleID
multi.t.test	multi.t.test
Protein Groups information extract.	P.G.extract
rename_dupnewID	rename_dupnewID
single_mod_enrichplot	single_mod_enrichplot
SoftThresholdScaleGraph	SoftThresholdScaleGraph
wgcnatest	wgcnatest