Package: protGear 1.17.0

Kennedy Mwai

protGear: Protein Micro Array Data Management and Interactive Visualization

A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.

Authors:Kennedy Mwai [cre, aut], James Mburu [aut], Jacqueline Waeni [ctb]

protGear_1.17.0.tar.gz
protGear_1.17.0.zip(r-4.7)protGear_1.17.0.zip(r-4.6)protGear_1.17.0.zip(r-4.5)
protGear_1.17.0.tgz(r-4.6-any)protGear_1.17.0.tgz(r-4.5-any)
protGear_1.17.0.tar.gz(r-4.7-any)protGear_1.17.0.tar.gz(r-4.6-any)
protGear_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
protGear/json (API)

# Install 'protGear' in R:

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

Bug tracker:https://github.com/keniajin/protgear/issues

On BioConductor:protGear-1.17.0(bioc 3.24)protGear-1.16.0(bioc 3.23)

microarray onechannel preprocessing biomedicalinformatics proteomics batcheffect normalization bayesian clustering regression systemsbiology immunooncology background-correction microarray-data normalisation proteomics-data shiny shinydashboard

4.34 score 1 stars 11 scripts 28 exports 191 dependencies

Last updated from:d855f9b210. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	215
linux-devel-x86_64	NOTE	326
source / vignettes	OK	360
linux-release-x86_64	NOTE	312
macos-release-arm64	NOTE	166
macos-oldrel-arm64	NOTE	207
windows-devel	NOTE	217
windows-release	NOTE	237
windows-oldrel	NOTE	237
wasm-release	OK	217

Exports:array_vars best_CV_estimation bg_correct buffer_spots check_sampleID_files create_dir cv_by_sample_estimation cv_estimation extract_bg launch_protGear_interactive launch_select matrix_normalise merge_sampleID minpositive name_of_files output_trend_stats plot_bg plot_buffer plot_FB plot_normalised plot_normalised_antigen read_array_files read_array_visualize rlm_normalise rlm_normalise_matrix tag_subtract visualize_slide visualize_slide_2d

Dependencies:abind affy affyio annotate AnnotationDbi askpass backports base64enc Biobase BiocGenerics BiocManager Biostrings bit bit64 blob boot broom bslib cachem car carData cli clipr cluster colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dendextend Deriv digest doBy dplyr DT ellipse emmeans estimability evaluate factoextra FactoMineR farver fastmap flashClust flexdashboard fontawesome forcats forecast Formula fracdiff fs genefilter generics GGally ggplot2 ggpubr ggrepel ggsci ggsignif ggstats ggtext glue gridExtra gridtext gtable gtools highr hms htmltools htmlwidgets httpuv httr IRanges irlba isoband jpeg jquerylib jsonlite KEGGREST Kendall knitr labeling later lattice lazyeval leaps lifecycle limma litedown lme4 lmtest magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr multcompView mvtnorm nlme nloptr nnet numDeriv openssl otel patchwork pbkrtest pheatmap pillar pkgconfig plotly plyr png polynom preprocessCore prettyunits progress promises purrr quantreg R.cache R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas remotes rlang rmarkdown rprojroot RSQLite rstatix S4Vectors S7 sass scales scatterplot3d Seqinfo shiny shinydashboard showtext showtextdb sourcetools SparseM statmod stringi stringr styler survival sys sysfonts tibble tidyr tidyselect timeDate tinytex tzdb urca utf8 vctrs viridis viridisLite vroom vsn withr xfun XML xml2 xtable XVector yaml zoo

protGear vignette processing suite

Rendered fromvignette.Rmdusingknitr::rmarkdown

Last update: 2022-12-11
Started: 2021-07-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
List the array structure variables	array_vars
best CV estimation	best_CV_estimation
bg_correct	bg_correct
Extract buffer spots of data	buffer_spots
\\_End_Function_\\ # Check existing sample ID names	check_sampleID_files
Title Create directory function	create_dir
cv by sample	cv_by_sample_estimation
cv_estimation	cv_estimation
extract bg	extract_bg
launch_protGear_interactive	launch_protGear_interactive
launch_select	launch_select
Normalize Arrays	matrix_normalise
Merge sample ID with the array data	merge_sampleID
Get the minimum positive value	minpositive
Object names of a list	name_of_files
Trend test using Cox–Stuart (C–S) and Mann–Kendall (M–K) trend tests	output_trend_stats
Plot background	plot_bg
Plot the buffer values	plot_buffer
plot_FB	plot_FB
Comparison of normalised data by sample	plot_normalised
Comparison of normalised data by feature	plot_normalised_antigen
Read array files	read_array_files
Read a gpr file to visualize	read_array_visualize
Nomrmalise using RLM	rlm_normalise_matrix
tag_subtract	tag_subtract
Visualize the slide mimicking the original scan image.	visualize_slide
Visualize the slide mimicking the original scan image using a 2d plot.	visualize_slide_2d