Installation

The easiest way to install scanRBP is by running:

pip install scanRBP

Note

On some systems, pip installs the executable scripts under ~/.local/bin. However this folder is not in the PATH, which will result in command not found if you try to run scanRBP on the command line. To fix this, run export PATH="$PATH:~/.local/bin" (and add this to your .profile). Another option is to install inside a virtual environment (using virtualenv).

If you would instead like to install the latest development version from this repository:

# clone the scanRBP GitHub repository
git clone https://github.com/grexor/scanRBP.git

# build and install
./build.sh

The motif database

On first use, scanRBP automatically downloads its PWM database — mCross eCLIP motifs plus CISBP-RNA motifs, about 6 MB — to ~/scanRBP_data. Nothing to configure for a default setup; see Motif database & search if you want to store it somewhere else.

scanRBP depends on pybio for FASTA/bedGraph reading, and on scipy/biopython/seaborn/matplotlib for scoring and plotting — all installed automatically by pip install scanRBP. See Dependencies.