klmr

# Command line tools don’t want to clutter their output with unnecessary noise.
library = function (...)
    suppressMessages(base::library(...))

#' The command line arguments
args = commandArgs(trailingOnly = TRUE)

#' The name of the script
#'
#' @note If the script was invoked interactively, this is the empty string.

klmr

library(dplyr)

counts = data.frame(Gene = c('A', 'B', 'C', 'D'),
                    Length = 1:4,
                    do1 = c(10, 20, 30, 40),
                    do2 = c(20, 40, 60, 80),
                    do3 = c(20, 20, 30, 40))

tpm = counts %>%
    mutate_each(funs(. / Length), starts_with('do')) %>%

klmr

package demo;

public class Numbers {
    static final String hexDigits = "0123456789ABCDEF";
    static final String decDigits = "0123456789";

    static int fromBaseRepresentation(final String value, final String digits) {
        final int base = digits.length();
        int result = 0;
        for (final char c : value.toCharArray()) {

klmr

#!/usr/bin/env Rscript
options(stringsAsFactors = FALSE)
library(dplyr)
library(ggplot2)
library(jsonlite)

# Usage:
# ./tagviews.r datafile.json output.png

args = commandArgs(TRUE)

klmr

Keybase proof

I hereby claim:

• I am klmr on github.
• I am klmr (https://keybase.io/klmr) on keybase.
• I have a public key whose fingerprint is C50E C91D 5CB6 5576 F218 02A7 819B 7ADF DFF6 82BE

To claim this, I am signing this object:

klmr

`^` = function (a, b) UseMethod('^')
`^.default` = .Primitive('^')
`^.character` = function (str, n) paste(rep(str, n), collapse = '')
'ho' ^ 3
# "hohoho"

klmr

memoize = function (f) {
    force(f)
    cache = new.env()
    function (...) {
        key = capture.output(dput(list(...)))
        if (key %in% ls(cache))
            return(get(key, envir = cache))

        value = f(...)
        assign(key, value, envir = cache)

klmr

library(biomaRt)
ensembl = useMart('ensembl', dataset = 'mmusculus_gene_ensembl')

seq = getBM(c('ensembl_gene_id', 'ensembl_transcript_id', 'coding'),
            filters = 'external_gene_name', values = 'HAT1', mart = ensembl)

head(seq, 1)

klmr

{
    "Browse Mode" = 3;
    CalSuccessfulLaunchTimestampPreferenceKey = "3.580207e+08";
    "Calculator Results Display" = 1;
    "Check for Update Frequency" = 1;
    "Check for Updates" = 1;
    "Delay Before Quitting" = 1;
    "Hide Dock Icon" = 1;
    "Last Update Check" = "2014-10-22 16:06:08 +0000";
    "Last Used Location" = "/Applications/Quicksilver.app";

klmr

read.table = function (file, ..., text) {
    args = list(...)
    if (missing(file))
        return(do.call(utils::read.table, c(args, text = text)))

    if (! ('sep' %in% names(args))) {
        separators = list('.csv' = ',',
                          '.tsv' = '\t',
                          '.txt' = '\t')
        extension = stringr::str_match(file, '(\\.\\w+)$')[, 2]