oganm

library(dplyr)

diamonds = ggplot2::diamonds

filterBy = 'color'
diamonds %>% filter(!!rlang::sym(filterBy) == 'E')

diamonds %>% group_by(!!rlang::sym(filterBy))

diamonds %>% mutate(!!rlang::sym('new_col'):='yes')

oganm

library(OpenImageR)
library(oro.dicom)
library(dplyr)
library(magrittr)
library(magick)

dicompath = '/home/omancarci/Dropbox/MRI'

imageFiles = list.files(file.path(dicompath,'DICOM'),recursive = TRUE,full.names = TRUE)

oganm

library(dplyr)

# available names stolen from https://github.com/moby/moby/blob/master/pkg/namesgenerator/names-generator.go----------------------
left = c("admiring",
         "adoring",
         "affectionate",
         "agitated",
         "amazing",
         "angry",
         "awesome",

oganm

getGithubFile = function(githubPath,branch = 'master', downloadPath = NULL,token = NULL){
    if(is.null(downloadPath)){
        downloadPath = tempfile()
    }
    
    path = strsplit(githubPath,'/')[[1]]
    file = paste(path[3:length(path)], collapse = '/')
    contents = gh::gh('GET /repos/:username/:reponame/contents/:dir?ref=:branch',
                  username = path[1],
                  reponame = path[2],

oganm

# this is to get data from a single git repository

library(dplyr)
library(anytime)
library(patchwork)
library(ggplot2)

commits = git2r::commits()

commitTime= commits %>% sapply(function(x){x$author$when$time}) %>% anytime

oganm

library(magrittr)
library(dplyr)
library(homologene) 
library(gemmaAPI) #  github.com/pavlidisLab/gemmaAAPI.R
library(markerGeneProfile) # github.com/pavlidisLab/markerGeneProfile
data("mouseMarkerGenesCombined")

# get mouse homologues of the hitlist
hitlist = readxl::read_xlsx('gene of interest.xlsx',col_names = FALSE) %>% 
  unlist %>% human2mouse %$% mouseGene

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),

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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(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

# 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')