slowkow

library(uwot)
library(scattermore)
library(foreach)
library(doParallel)
library(data.table)
library(ggplot2)
library(scales)
library(glue)

# This code snippet assumes we have these objects:

marcc-hpc

#!/bin/bash

# this module is specific to MARCC
module load anaconda-python/3.6

# create anaconda environment and use it
conda create -y -n sircel python
source activate sircel

# install kallisto, redis

rccordell

# This script builds on Aleszu Bajak's excellent 
# [tutorial on building a course website using R Markdown and Github pages](http://www.storybench.org/convert-google-doc-rmarkdown-publish-github-pages/). 
# I was excited about the concept but wanted to automate a few of the production steps: namely generating the HTML files 
# for the site from the RMD pages (which Aleszu describes doing one-by-one) and generating the site navigation menu, 
# which Aleszu handcodes in the `_site.yml` file. This script should automate both processes, though it may have some quirks 
# unique to my setup that you'd want to tweak to fit your own. It's likely more loquacious than necessary as well, so feel free 
# to condense as you can. Ideally, each time you make updates to your RMD files you can run this script to generate updated HTML 
# pages and a new `_site.yml`. Then commit changes to Github and you're up and running!

# Once you've got everything configured for your own site below, you should be able to run `source('rend

pierrejoubert73

How to add a collapsible section in markdown

1. Example

Click me

Heading

1. Foo
2. Bar
   • Baz

• Qux

martinbuberl

Import an Existing Git Repository into Another

Before: Folder Structure (Two Separate Repositories)

XXX
 |- .git
 |- (project files)
YYY
 |- .git

mikelove

accession2url <- function(x) {
  prefix <- "ftp://ftp.sra.ebi.ac.uk/vol1/fastq"
  dir1 <- paste0("/",substr(x,1,6))
  dir2 <- ifelse(nchar(x) == 9, "",
          ifelse(nchar(x) == 10, paste0("/00",substr(x,10,10)),
          ifelse(nchar(x) == 11, paste0("/0",substr(x,10,11)),
                                 paste0("/",substr(x,10,12)))))
  paste0(prefix,dir1,dir2,"/",x)
}

calstad

Quick List of Resources for Topological Data Analysis with Emphasis on Machine Learning

This is just a quick list of resourses on TDA that I put together for @rickasaurus after he was asking for links to papers, books, etc on Twitter and is by no means an exhaustive list.

Survey Papers

Both Carlsson's and Ghrist's survey papers offer a very good introduction to the subject

• Topology and Data by Gunnar Carlsson
• Barcodes: The Persistent Topology of Data by Robert Ghrist

Other Papers and Web Resources

• Extracting insights from the shape of complex data using topology A good introductory paper in Nature on the Mapper algorithm.

pbugnion

This gist lets you keep IPython notebooks in git repositories. It tells git to ignore prompt numbers and program outputs when checking that a file has changed.

To use the script, follow the instructions given in the script's docstring.

For further details, read this blogpost.

The procedure outlined here is inspired by this answer on Stack Overflow.