oganm

#!/usr/bin/env Rscript

library(magrittr)
library(reshape2)

d <- read.csv("FINAL LAB DATA Mar 23 2017.csv", colClasses="character", fileEncoding = "UTF-8-BOM")
d <- d[order(d$ID),]

# assign each visit a number (per patient)
visit.numbers <- tapply(d$Collection.Date, d$ID, function (x) 

oganm

{
  "data": [
    {
      "name": "050512MJA_U133_2.0_IB29.CEL",
      "description": "",
      "sequencePairedReads": null,
      "sequenceReadCount": null,
      "sequenceReadLength": null,
      "outlier": false,
      "metadata": null,

oganm

devtools::install_github('oganm/neuroExpressoAnalysis')
library(neuroExpressoAnalysis)
devtools::install_github('oganm/ogbox')
library(ogbox)
devtools::install_github('oganm/markerGeneProfile')
library(markerGeneProfile)

library(scales)
library(gplots)
library(stringr)

oganm

extendShinyjsEvenFurther = function(){
    jscode <- '
Shiny.addCustomMessageHandler("mymessage", function(message) {
    eval(message);
});
    '
    tags$head(tags$script(HTML(jscode)))
}

jsExecute = function(jscode,session){

oganm

library(shiny)
library(shinyWidgets)

moduleUI = function(id){
    ns = NS(id)
    
    tagList(actionButton(inputId = ns('update'),label = 'update'),
            progressBar(id = "progressBar", value = 50),
            checkboxInput(inputId = ns('checkbox'),label = 'shinyCheckbox',value = FALSE))
}

oganm

library(stringr)
library(magrittr)
library(pdftools)
library(Hmisc)

capitalizeAll = function(x){
    words = strsplit(x, ' ') %>% {.[[1]]}
    capital = sapply(words, function(x){
        if(x %in% c('for','of','and','to','into','with','the','from','via')){
            return(x)

oganm

# ontologyPlot package requires bioconductor package Rgraphvis
# source("https://bioconductor.org/biocLite.R")
# biocLite("Rgraphvis")
# install.packages('ontologyIndex')
# install.packages('ontologyPlot')

library(ontologyIndex)
library(ontologyPlot)

download.file(url = 'http://purl.obolibrary.org/obo/uberon.obo',destfile = 'uberon.obo')

oganm

library(CellCODE)
library(dplyr)
library(purrr)
library(magrittr)
library(markerGeneProfile)
data('mouseMarkerGenesCombined')

# this function will turn gene lists into CellCODE inputs
cellCodeInput = function(genes){
    geneCount = genes %>% map(length)

oganm

regions = c('Cortex','Hippocampus','Striatum','Cerebellum','Thalamus')


regions %>% lapply(function(x){
    cellTypes = names(mouseMarkerGenesCombined[[x]])
    cellTypes %>% lapply(function(y){
        data.frame(symbol = mouseMarkerGenesCombined[[x]][[y]], NCBIid = mouseMarkerGenesCombinedNCBI[[x]][[y]])
    })

})

oganm

library(import5eChar)
library(purrr)
library(ogbox)
library(dplyr)
library(ggplot2)
library(stringr)
library(igraph)
library(glue)
library(cowplot)
charFiles = c(list.files('/srv/shiny-server/printSheetApp/chars/',full.names = TRUE),