oganm

library(gemma.R)
library(ggplot2)
library(magrittr)
library(dplyr)


# mouse Eno2 datasets that are annotated with the term for brain
brain_eno2 = get_gene_differential_expression_values(13807 , uris = "http://purl.obolibrary.org/obo/UBERON_0000955")

oganm

library(readxl)
library(writexl)
library(gemma.R)
library(GEOquery)
library(dplyr)
library(glue)

data = readxl::read_excel('~/Downloads/Bad_QC_datasets_together.xlsx')

datasets = data$dataset

oganm

devtools::load_all()
library(magrittr)
datasets <- get_datasets(uris = 'http://purl.obolibrary.org/obo/MONDO_0000408')
relevant_terms <- attributes(datasets)$filter %>% stringr::str_extract_all('http.*?(?=,|\\))') %>% {.[[1]]}

relevant_terms %<>% c('http://purl.obolibrary.org/obo/CHEBI_16236')


dataset_contrasts <- datasets$experiment.shortName %>% 
    lapply(function(x){

oganm

library(RCurl)
library(xml2)
library(dplyr)
library(stringr)

obsolete <- readr::read_tsv('obsolete-terms.txt')


# get our ontology files
ontologies <- system2("ssh" ,paste0(ontology_server," ls ", ontology_path),stdout = TRUE)

oganm

library(chromote)

startRoll20Session = function(email, password, gameLink,view = FALSE){
  
  b <- chromote::ChromoteSession$new()
  if(view){
    b$view()
  }
  b$Page$navigate(gameLink)
  b$DOM$enable()

oganm

library(gemmaAPI)

# identify all yeast datasets
yeastStudies  = taxonInfo('yeast',request = 'datasets',limit = 0)

studyIDs = yeastStudies %>% purrr::map_chr('id')

# get metadata for yeast studies
yeastMetadata = studyIDs %>% lapply(compileMetadata,outputType = 'list') 

oganm

# source https://en.wikipedia.org/wiki/Flag_of_Turkey

# suggested width for narrow images
coverWidth = 590

starOverlap = 2/5-1/3

# approximate and arbitrary
G = coverWidth* (4/3 - starOverlap)

oganm

#!/usr/bin/Rscript
# Rscript install.R packageName
# point of this is to be able to install arbitrary packages from CRAN, github, bioconductor, etc from command line
# used for my remote server where I use the root library to share packages between my user and the shiny user
# sudo install.R glue oganm/ogbox bioc::3.6/affy

library(dplyr)
library(ogbox)

print(.libPaths())

oganm

library(cranlogs)
library(dplyr)

allPackages = available.packages() %>% rownames

groups = cut(seq_along(allPackages), breaks = seq(0,length(allPackages),20)) %>% {.=as.character(.);.[is.na(.)]='last';factor(.,levels = unique(.))}
package_groups = split(allPackages,groups)


package_groups %>% lapply(function(x){

oganm

library(rayshader)
library(ambient)


k = 8
m = noise_perlin(dim = c(2^k,2^k),octaves = 9)
mToMap(m)

m = noise_simplex(c(2^k,2^k),fractal = 'fbm',octaves = 4,lacunarity = 2,gain = .5,frequency = .01)