stephenturner

// Place your key bindings in this file to overwrite the defaults
[
    // RStudio: Copy lines up/down with alt+cmd+up/down
    {
        "key": "alt+cmd+down",
        "command": "editor.action.copyLinesDownAction",
        "when": "editorTextFocus && !editorReadonly"
    },
    {
        "key": "shift+alt+down",

stephenturner

# R session 1: model training and deployment ------------------------------

library(tidymodels)
library(vetiver)
library(plumber)

# Not the way you'd actually split data - for demo only
cars_train <- mtcars[1:24,]
cars_test <- mtcars[25:32,]

stephenturner

#!/usr/bin/env python 

# Adds allelic depth (AD)=2 to a VCF.
# Usage: bcftools view my.vcf.gz | addad.py | bcftools sort -Oz -o my.ad.vcf.gz && tabix my.ad.vcf.gz
 
import pysam

vcf_in=pysam.VariantFile("-","r")

vcf_in.header.formats.add("AD",".","Integer","Allelic depth, hard-coded as 2")

stephenturner

# Start window and pane indices at 1 instead of 0
set -g base-index 1
set -g pane-base-index 1

# Shift arrow keys to move around panes
bind -n S-Up    select-pane -U
bind -n S-Down  select-pane -D
bind -n S-Left  select-pane -L
bind -n S-Right select-pane -R

stephenturner

n <- 1e7
x <- sample(n, size=n, replace=TRUE)
length(unique(x))/n
# [1] 0.6321897
1-exp(-1)
# [1] 0.6321206

stephenturner

# Compile and install htslib, bcftools, samtools 1.9 to home directory

# Set up dirs where stuff will be installed
mkdir -p ${HOME}/bin/htslib
mkdir -p ${HOME}/bin/bcftools
mkdir -p ${HOME}/bin/samtools

# Make a dir to build
mkdir -p ${HOME}/tmp

stephenturner

# Load some packages
library(knitr)
library(tidyverse)
library(DT)

# Get licenses for all installed packages.
installed_licenses <- installed.packages() %>% 
  as.data.frame() %>% 
  rownames_to_column("package") %>% 
  as_tibble() %>% 

stephenturner

#!/usr/bin/perl

use warnings;
use strict;

use Getopt::Long;
Getopt::Long::Configure('bundling');

my ($verbose, $no_act, $force, $op);

stephenturner

have <- tibble::tribble(
  ~id1, ~id2, ~value,
   "a",  "b",     1L,
   "c",  "a",     2L,
   "c",  "b",     3L
  )
have

want <- tibble::tribble(
  ~id1, ~id2, ~value,

stephenturner

[
    {
        "name": "Sci-Hub Lookup",
        "alias": "Sci-Hub",
        "icon": "null",
        "_urlTemplate": "https://sci-hub.tw/{z:DOI}",
        "description": "Sci-Hub full text PDF search",
        "hidden": false,
        "_urlParams": [],
        "_urlNamespaces": {