2 Download and Installation

2.0.0.1 System requirements and configuration

  • We recommend running Ryabhatta and Natian on Windows, Machintosh or Linux machines with at least 30 GB free storage, 4 GB or more of RAM, and 2-4 cores of CPU.

Large datasets of > 35000 cells or using multiple datasets of comparable size might require higher RAM for better experience.

Processing steps such as dimensionality reduction, scaling data, finding markers in Natian and monocle pseudotime analysis in Ryabhatta can benefit from running on a system with higher RAM (high performance clusters).

2.1 No install, ready-to-use app.

2.2 Version that requires installation.

  • Please go to singlecelltranscriptomics.org for the latest version of the apps, and example data as a zipped file.

  • Extract the files using an unzip tool on your computer.

2.2.0.1 Install R, RStudio, and other dependencies

  1. Install R :
    • To install R, go to r-project click on the download R link.
    • Select the CRAN mirror that you would like to use for downloading R.
    • Next, click on the R version that is compatible with your operating system.
    • Then click on install R for the first time .
    • From the same place, you can also install R tools (> version 39) for best experience with Ryabhatta and Natian on Windows.

  2. Install RStudio :
    • To install RStudio, go to rstudio.com and click on the Download link on the top right.
    • Choose the version suits you. Ryabhatta and Natian can run in Rstudio Desktop and RStudio server in both the professional and the free versions

  3. Install package dependencies :
    • Once you have installed R and RStudio, run Rstudio
    • In RStudio, use File > open file to open the file install_ryabhatta.r from the downloaded package.
    • Once the file opens, click on source button on the top right corner of the left-hand panel.
    • This will generate a prompt on the console panel in the bottom:
      Do you wish to install Ryabhatta dependencies (y/n)?
    • please press “y” and press “enter” key
    • The second prompt will inquire if you wish to install the dependencies in a separate folder:
      Do you wish to create a new folder and install all of the packages into the new folder library (y/n)?
    • press “y” or “n” according to your choice and press “enter”

Install packages in a new folder: if you do not wish to overwrite existing packages used for other project. Natian and Ryabhatta will automatically use the new library installed in the new folder.

Prompts about installing binaries: if you run into RStudio prompts about installing binaries instead of source, please press “Yes” or “No” depending to continue to the process.

2.2.0.2 Additional system requirements

  • For Machintosh users, there may be a need to install the binary version of the XML pacakge. In this case please authorize the installation of the binary verison

  • To get the best experience, Mac users can install XQuartz for the Cairo package used to download high-resolution PDFs. Download Xquartz from https://www.xquartz.org/

  • The new version of OSX also disables the Arial font. This needs to be enabled using the Fontbook application on Macintosh machines. You can do so, following the instructions on this link

2.3 Reporting issues