Package: oppti 1.21.0

Abdulkadir Elmas

oppti: Outlier Protein and Phosphosite Target Identifier

The aim of oppti is to analyze protein (and phosphosite) expressions to find outlying markers for each sample in the given cohort(s) for the discovery of personalized actionable targets.

Authors:Abdulkadir Elmas

oppti_1.21.0.tar.gz
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oppti.pdf |oppti.html✨
oppti/json (API)
NEWS

# Install 'oppti' in R:

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

Bug tracker:https://github.com/huang-lab/oppti/issues

On BioConductor:oppti-1.21.0(bioc 3.21)oppti-1.20.0(bioc 3.20)

proteomics regression differentialexpression biomedicalinformatics genetarget geneexpression network

4.30 score 2 stars 2 scripts 132 downloads 10 exports 117 dependencies

Last updated 2 months agofrom:1c8e74d516. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	WARNING	Nov 29 2024
R-4.5-linux	WARNING	Nov 29 2024
R-4.4-win	WARNING	Nov 29 2024
R-4.4-mac	WARNING	Nov 29 2024
R-4.3-win	WARNING	Nov 29 2024
R-4.3-mac	WARNING	Nov 29 2024

Exports:artImpute clusterData dropMarkers dysReg markOut oppti outScores plotDen rankPerOut statTest

Dependencies:askpass base64enc brew brio bslib cachem callr cli clipr colorspace commonmark cpp11 crayon credentials curl desc devtools diffobj digest downlit ellipsis evaluate fansi farver fastmap fontawesome fs gert ggplot2 gh gitcreds glue gtable highr htmltools htmlwidgets httpuv httr2 ini isoband jquerylib jsonlite knitr labeling later lattice lifecycle limma magrittr MASS Matrix memoise mgcv mime miniUI munsell nlme openssl parallelDist pheatmap pillar pkgbuild pkgconfig pkgdown pkgload plyr praise prettyunits processx profvis promises ps purrr R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RcppArmadillo RcppParallel remotes reshape rlang rmarkdown roxygen2 rprojroot rstudioapi rversions sass scales sessioninfo shiny sourcetools statmod stringi stringr sys systemfonts testthat textshaping tibble tinytex urlchecker usethis utf8 vctrs viridisLite waldo whisker withr xfun xml2 xopen xtable yaml zip

Outlier Protein and Phosphosite Target Identifier

Rendered fromanalysis.Rmdusingknitr::knitron Nov 29 2024.

Last update: 2021-08-27
Started: 2019-07-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Artificially miss and impute each data entry individually by ignoring outlying values	artImpute
Hierarchical cluster analysis	clusterData
Filter out markers	dropMarkers
Analyze dysregulated (protruding) events	dysReg
Display outlying expressions	markOut
Outlier protein and phosphosite target identification	oppti
Analyze putative outliers	outScores
Draw densities	plotDen
Rank markers by the percentage of outlying events	rankPerOut
Analyze dysregulation significance	statTest