neilfws

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neilfws

---
title: "ztable"
author: "Neil Saunders"
date: "19 March 2019"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

neilfws

# function to make the cloud
# assumes rtweet authentication configured as per documentation

make_tweetcloud <- function(user = "neilfws", tweets = 100) {
  require(tidyverse)
  require(tidytext)
  require(rtweet)
  require(wordcloud)
  
  get_timeline(user, n = tweets, full_text = TRUE) %>% 

neilfws

# taken from the fifer package
# https://github.com/dustinfife/fifer

excelCols <- function (n) 
{
  vec1 = LETTERS
  if (n <= 26) {
    res = vec1[seq_len(n)]
  }
  else if (n > 26 & n <= 702) {

neilfws

library(httr)

req <- POST("http://mappify.io/api/rpc/address/geocode/", 
            body = list(streetAddress = "252 Botany St", 
                        suburb = "Sydney", 
                        postCode = "2000", 
                        state = "NSW"), 
            encode = "json")

res <- content(req, "parsed")

neilfws

library(rentrez)

# search for "epigenetics"
es <- entrez_search("pubmed", "epigenetics")
es$count
[1] 20759

# search for "epigenetics" published in 2014
# for all publications in 2014 just drop the "epigenetics"
es <- entrez_search("pubmed", "epigenetics 2014[dp]")

neilfws

# taken from http://sciencecases.lib.buffalo.edu/cs/files/mini_eco_stats.pdf
#
# NATIONAL CENTER FOR CASE STUDY TEACHING IN SCIENCE
# Mini Cases on Choosing Appropriate
# Statistical Tests for Ecological Data
# by
# Alyssa M. Gleichsner, Department of Biological Sciences
# Elizabeth A. Flaherty, Department of Forestry and Natural Resources
# Purdue University, West Lafayette, IN
# Instructions

neilfws

# pmid2bibtex.rb
# convert a PubMed PMID to BibTeX citation format
# updated version of http://chrisamiller.com/science/2010/12/13/using-bioruby-to-fetch-citations-from-pubmed/
# works as of 2015-03-18

require 'bio'
Bio::NCBI.default_email = "me@me.com" # required for EUtils

id  = "18265351"
pm  = Bio::PubMed::efetch(id)         # array of MEDLINE-formatted string

neilfws

gse <- getGEO("GSE45016") # you want GSEMatrix = TRUE

# ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45016/matrix/
# Found 1 file(s)
# GSE45016_series_matrix.txt.gz
# trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45016/matrix/GSE45016_series_matrix.txt.gz'
# ftp data connection made, file length 1486394 bytes
# opened URL
# ==================================================
# downloaded 1.4 Mb

neilfws

Here are the names of the deb packages that you can *sudo apt-get install* on Ubuntu-like systems, 
to install Perl dependencies for biopieces:

libmodule-build-perl
libbit-vector-perl
libsvg-perl
libterm-readkey-perl
libdbi-perl
libxml-parser-perl
libcarp-clan-perl