@@ -5,6 +5,7 @@ Version: 0.99.1

 Authors@R: c(person("Kennedy", "Mwai", role = c("cre", "aut"), email = "keniajin@gmail.com"),

              person(c("James", "Mburu"), role = "aut" , email = "mburuwanja@gmail.com") ,

              person(c("Jacqueline", "Waeni"), role = "ctb" , email = "jacqwaeni@gmail.com"))

+Maintainer: K Mwai <keniajin@gmail.com>

 Description: 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.

 License: GPL-3

 URL: https://github.com/Keniajin/protGear

@@ -18,7 +19,7 @@ Imports:

     shiny (>= 1.0.0) , trend (>= 1.1.4),  purrr (>= 0.3.4),  plotly (>= 4.9.0) , MASS (>= 7.3) , 

     htmltools (>= 0.4.0) , flexdashboard (>= 0.5.2) , shinydashboard (>= 0.7.1) , kableExtra (>= 1.3.4), GGally (>= 2.1.2) , pheatmap (>= 1.0.12) , png (>= 0.1-7) , grid(>= 4.1.1),

      styler (>= 1.6.1) , factoextra (>= 1.0.7) ,FactoMineR (>= 2.4) , magick (>= 2.7.3) , rlang (>= 0.4.11),

-     ggplotify (>= 0.1.0) , remotes (>= 2.4.0)

+     ggplotify (>= 0.1.0) , remotes (>= 2.4.0) , factoextra (>= 1.0.7)

 biocViews: Microarray, OneChannel, Preprocessing , BiomedicalInformatics , Proteomics , BatchEffect, Normalization

 Encoding: UTF-8

 LazyData: false

@@ -13,7 +13,7 @@ runtime: shiny

 ```{r setup, include=FALSE}

 ## Inside the working directory create a sampleID folder to contain information of the sampleIDs

 ## they should be named according to the sampleID names

-pac_loads <- c('tidyverse','ggpubr','limma','vsn','ggpubr','gtools','plotly','shinythemes','shinyjs','shinyWidgets','GGally' ,'DT',   'shinycssloaders', 'gridExtra','pheatmap','scales','shinyFeedback','shinyalert', 'data.table','stringr', 'trend',   'flexdashboard', 'shiny')

+pac_loads <- c('tidyverse','ggpubr','limma','vsn','ggpubr','gtools','plotly','shinythemes','shinyjs','shinyWidgets','GGally' ,'DT',   'shinycssloaders', 'gridExtra','pheatmap','scales','shinyFeedback','shinyalert', 'data.table','stringr', 'trend',   'flexdashboard', 'shiny','factoextra')

 sapply(pac_loads, require, character.only = TRUE)

@@ -26,8 +26,26 @@ output:

 ```{r setup, include=FALSE}

-ploads <- c('tidyverse','ggpubr','gtools','purrr','scales','pheatmap', 'data.table','kableExtra','gridExtra', 'png','knitr' ,'grid','styler',  'factoextra','FactoMineR','magick','rlang','GGally','ggplotify', 'remotes')

-sapply(ploads, require, character.only = TRUE)

+library(ggpubr)

+library(gtools)

+library(purrr)

+library(scales)

+library(pheatmap)

+library(data.table)

+library(kableExtra)

+library(gridExtra)

+library(png)

+library(knitr)

+library(grid)

+library(styler)

+library(FactoMineR)

+library(factoextra)

+library(magick)

+library(rlang)

+library(GGally)

+library(ggplotify)

+library(remotes)

+

 knitr::opts_chunk$set(echo = TRUE, message=FALSE,warning = FALSE,

                       fig.align = 'center',#tidy = T,tidy.opts=list(arrow=TRUE, indent=2),

                       dev = "png", dev.args = list(type = "cairo-png"),