# Command-line and RStudio

Overview and discussion of the previous three lessons:

([Running BLAST at the command line](running-command-line-blast.html),
[Running large scale BLASTs and output.](running-blast-large-scale.html),
[Visualizing BLAST score distributions in RStudio](visualizing-blast-scores-with-RStudio.html))

The
[Software Carpentry shell lesson](https://swcarpentry.github.io/shell-novice/)
is good for people to go through, either collectively or individually.

Questions to discuss and address:

* where are the files and directories that we are accessing at the shell?

* where are the files and directories that we are accessing via RStudio Web?

* related: why am I using R via a Web interface rather than on my local
  computer?

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We will cover more R on Thursday morning, where we will go through
[Manipulating and analyzing data with dplyr](http://www.datacarpentry.org/R-ecology-lesson/03-dplyr.html).