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View keybase.md

Keybase proof

I hereby claim:

  • I am kippjohnson on github.
  • I am kippp (https://keybase.io/kippp) on keybase.
  • I have a public key ASBBGwy60nktkTN-Q5zxTA9io6vTJdT4eNXWIwtzWp-pBgo

To claim this, I am signing this object:

View bnn
{"nodes":[{"name":" Andrew Kasarskis","ntimes":7,"id":" Andrew Kasarskis"},{"name":" Atul J Butte","ntimes":8,"id":" Atul J Butte"},{"name":" Ben Readhead","ntimes":12,"id":" Ben Readhead"},{"name":" Bin Chen","ntimes":5,"id":" Bin Chen"},{"name":" Brian A Kidd","ntimes":4,"id":" Brian A Kidd"},{"name":" Eric E Schadt","ntimes":6,"id":" Eric E Schadt"},{"name":" Jagat Narula","ntimes":5,"id":" Jagat Narula"},{"name":" Khader Shameer","ntimes":18,"id":" Khader Shameer"},{"name":" Li Li","ntimes":18,"id":" Li Li"},{"name":" Marcus A Badgeley","ntimes":6,"id":" Marcus A Badgeley"},{"name":" Max S Tomlinson","ntimes":4,"id":" Max S Tomlinson"},{"name":" Riccardo Miotto","ntimes":5,"id":" Riccardo Miotto"},{"name":" Rong Chen","ntimes":13,"id":" Rong Chen"},{"name":" Samin K Sharma","ntimes":4,"id":" Samin K Sharma"},{"name":" Shameer Khader","ntimes":4,"id":" Shameer Khader"},{"name":" Yuliya Vengrenyuk","ntimes":6,"id":" Yuliya Vengrenyuk"},{"name":"Beau Norgeot","ntimes":4,"id":"Beau Norgeot"},{"name":"Benjamin
@kippjohnson
kippjohnson / R docker file
Created Aug 15, 2019
All packages are in CRAN versioned to R 3.6.1
View R docker file
FROM rocker/rstudio:3.6.1
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
libxml2-dev \
libcairo2-dev \
libsqlite3-dev \
libmariadbd-dev \
libmariadb-client-lgpl-dev \
libpq-dev \
libssh2-1-dev \
View saving_files.R
> rm(list=ls())
> set.seed(123)
> library(data.table)
> library(feather)
> library(tidyverse)
> dsize=1e7
> nc <- 100
> x <- data.frame(matrix(rnorm(dsize), ncol=nc))
> ###
> ### write.table
View plotting_code.R
library(data.table)
library(ggplot2)
library(ggsci)
dat <- fread("~/Downloads/neoplasm_vs_circulatory_mortality_parsed.txt")
colnames(dat) <- c("V0", "Gender", "GenderCode", "CauseOfDeath", "ICD", "Year", "Year1", "Deaths", "Population", "CrudeRate","AgeAdjustedRate")
dat$Cause <- plyr::mapvalues(dat$CauseOfDeath, from=c("Diseases of the circulatory system","Neoplasms"), to=c("Circulatory\nSystem","Neoplasm"))
ggplot(dat, aes(x=Year, y=CrudeRate, color=Gender, linetype=Cause)) +
geom_line() +
View neoplasm_vs_circulatory_mortality_parsed.txt
"Female" "F" "Neoplasms" "C00-D48" "1999" "1999" 270713 142237295 190.3 171.7
"Female" "F" "Neoplasms" "C00-D48" "2000" "2000" 273996 143368343 191.1 171.8
"Female" "F" "Neoplasms" "C00-D48" "2001" "2001" 273634 145077463 188.6 169.2
"Female" "F" "Neoplasms" "C00-D48" "2002" "2002" 275266 146394634 188.0 167.7
"Female" "F" "Neoplasms" "C00-D48" "2003" "2003" 275788 147679036 186.7 165.4
"Female" "F" "Neoplasms" "C00-D48" "2004" "2004" 273874 148977286 183.8 162.1
"Female" "F" "Neoplasms" "C00-D48" "2005" "2005" 275780 150319521 183.5 160.5
"Female" "F" "Neoplasms" "C00-D48" "2006" "2006" 276957 151732647 182.5 158.6
"Female" "F" "Neoplasms" "C00-D48" "2007" "2007" 276966 153166353 180.8 156.0
"Female" "F" "Neoplasms" "C00-D48" "2008" "2008" 277219 154604015 179.3 153.3
View identifying_countries_by_height_thought_experiment_computational_analysis.R
## Concerns thought experiment in
## Common sequence variants affect molecular function more than rare variants?
## https://www.nature.com/articles/s41598-017-01054-2.pdf
## page 8, first section of discussion
## Doesn't seem right.
rm(list=ls())
set.seed(123)
View get_merged_rsIDs.R
## Kipp Johnson
## Ugly code to find all potential merged rsIDs
rm(list=ls())
setwd('~/Dropbox/DudleyLab/chayakrit/pad_gwas/validation/')
## packages
library(data.table)
library(httr)
library(jsonlite)