Personal note: In the name of those Linux users who do not have/want MS-Word: Please make the effort of using .DOCX and not .DOC .DOCX is better supported in non-MS sofware.

Software I wrote

• RRHO R package: Implements the Rank-Rank Hypergeometric Overlap Test. Download from Bioconductor or Github.

• chords R Package: Estimate population size and degree distribution in respondent driven samples, presented in our paper. Download from CRAN

• SimpleLearner: Implements an easy to tune polynomial deep learning network. Download from GitHub.

• Scraping ArXiv: Script for scraping ArXiv meta data and doing some exploratory statistics of manuscript ArXiving. Download from github.

• SelectiveCI R package: Implements post-selection confidence intervals, presented in our paper. Download from github.

• FPF R Package: Finds the prevalence of activation in fMRI group studies, presented in our paper.

  • Download from R-Forge.
  • Link to tutorial.

Software I use

• Ubuntu- a friendly Linux distribution with Hebrew support.
• Data:
  • R- for programming with data. I also maintain the Israeli R user group.
  • RStudio Server running in the AWS cloud for data analysis (see my blogpost).
• Typesetting:
  • TexStudio for LaTeX editing.
  • bookdown for authoring articles, books, and reports.
• Version control: git with github for code, manuscripts, etc.
• Scribus- for scientific posters.
• Zotero- for managing references (I like Mendeley, PaperPile, and F1000Workplace, but I am already addicted).
• Calibre for managing my (e)book library.
• Reeder- by far my favorite RSS reader (since GoogleReader closed).
• Pocket- For all the “I want to read this later” sites.
• Jekyll with GitHub: for blogging.

Software I want to try but didn’t have the time yet:

• Mendeley or Paperpile for reference management.
• Julia.
• Python.

Hardware I use

• Server- Lenovo x3850-X6: Just because I find that the batch cluster computing paradigm (e.g. Condor, SGE, etc.) is not suited for modern interactive data analysis. I found that you can get much more done with a single, massive, multiple core, RAM rich, server (running RStudio Server obviously).

• Laptop- Lenovo T460s: The size of the X1 with the power of the T series.

• Cloud- AWS: For any ad-hoc hardware needs (which is quite often for me), I just start an EC2 instance.