stephenturner

This list is outdated. This post has a list of bioinformatics/genomics/genetics workshops and training materials that I haven't updated since 2015.

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In-person courses

Note that many of the courses shown below also have course materials from past years publicly available online.

Cold Spring Harbor Courses:

stephenturner

conda create -n gdc python=2.7 libxml2 libxslt libffi gcc progressbar
source activate gdc

git clone https://github.com/NCI-GDC/gdc-client
cd gdc-client
python setup.py install

stephenturner

SNP	CHR	BP	P
rs3094315	1	752566	0.5571
rs3131972	1	752721	0.4664
rs12562034	1	768448	0.7376
rs12124819	1	776546	0.6662
rs11240777	1	798959	0.9756
rs6681049	1	800007	0.9759
rs4970383	1	838555	0.2906
rs4475691	1	846808	0.07047
rs7537756	1	854250	0.04206

stephenturner

#!/usr/bin/python

import sys

header=True
for line in sys.stdin:
    if line.startswith('##'):
        if header:
            print line.strip()
        continue

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

[
    // Auto-pair backticks
  { "keys": ["`"], "command": "insert_snippet", "args": {"contents": "`$0`"}, "context":
    [
      { "key": "setting.auto_match_enabled", "operator": "equal", "operand": true },
      { "key": "selection_empty", "operator": "equal", "operand": true, "match_all": true },
      { "key": "following_text", "operator": "regex_contains", "operand": "^(?:\t| |\\)|]|\\}|>|$)", "match_all": true },
      { "key": "preceding_text", "operator": "not_regex_contains", "operand": "[`a-zA-Z0-9_]$", "match_all": true },
      { "key": "eol_selector", "operator": "not_equal", "operand": "string.quoted.single", "match_all": true }
    ]

stephenturner

<script language="JavaScript">
$(function() {
  /* Lets the user click on the images to view them in full resolution. */
  $("div.figure img").wrap(function() {
    var link = $('<a/>');
    link.attr('href', $(this).attr('src'));
    link.attr('title', $(this).attr('alt'));
    link.attr('target', '_blank');
    return link;
  });

stephenturner

## devtools::install_github("stephenturner/msigdf")
library(msigdf)
library(dplyr)
library(clusterProfiler)

c2 <- msigdf.human %>% 
    filter(collection == "c2") %>% select(geneset, entrez) %>% as.data.frame

data(geneList)
de <- names(geneList)[1:100]

stephenturner

# Performs principal components analysis on an ExpressionSet
eset_pca <- function (eset) {
  mypca <- prcomp(t(na.omit(exprs(eset))))
  pca <- as.data.frame(mypca$x)
  pc1var <- round(summary(mypca)$importance[2,1]*100, digits<-1)
  pc2var <- round(summary(mypca)$importance[2,2]*100, digits<-1)
  pc1lab <- paste0("PC1 (",as.character(pc1var),"%)")
  pc2lab <- paste0("PC1 (",as.character(pc2var),"%)")
  out <- merge(pData(eset), pca, by<-"row.names") %>% 
    dplyr::rename(id<-Row.names)

stephenturner

#!/bin/bash

# Nullarbor+dependencies installation script for a fresh Ubuntu 14.04 instance.


################################################################################
## Conveniences
################################################################################

# Some essential aliases