q2-PSEA

Qiime2 plugin used to accomplish Peptide Set Enrichment Analysis (PSEA) and visualize results.

Installation

Dependencies:

  • qiime2-2023.7 or later

  • q2-pepsirf

  • q2-ps-plot

  • altair v5.0.0 or later

  • altair_saver v0.5.0 or later

  • rpy2 v3.5.11 or later

R Dependencies:

  • r-base v4.2.2 or later

  • r-biocmanager

  • r-essentials v1.7.0 or later

  • r-igraph v1.4.2 or later

  • r-ggraph v2.1.0 or later

  • r-ggforce v0.4.1 or later

  • r-scatterpie v0.2.1 or later

  • r-splines2 v0.5.1 or later

  • bioconductor-ggtree v3.6.0 or later

  • bioconductor-enrichplot v1.18.0 or later

Qiime2 Installation:

Visit: https://docs.qiime2.org/2022.2/install/ for intallation documentation on Qiime2

q2-pepsirf Installation:

Visit: https://ladnerlab.github.io/pepsirf-q2-plugin-docs/Pepsirf_Plugins/q2-pepsirf1/ for installation documentation on q2-pepsirf

q2-ps-plot Installation:

Visit: https://ladnerlab.github.io/pepsirf-q2-plugin-docs/Pepsirf_Plugins/q2-ps-plot/ for installation documentation on q2-ps-plot

q2-PSEA Installation:

Make sure your Qiime2 conda environment is activated by running the command:

conda activate qiime2-2023.7

You can replace qiime2-2023.7 above with whichever version of QIIME 2 you have currently installed.

To help make installing R dependencies easier, please use this command if you have trouble:
conda install -c conda-forge r-base r-essentials r-igraph r-ggraph r-ggforce r-scatterpie rpy2 r-biocmanager r-splines2
conda install -c bioconda bioconductor-ggtree bioconductor-enrichplot
You will need to install clusterProfiler through R to avoid conflicting versions with some packages:
Please download the custom R script to do so here: https://github.com/LadnerLab/q2-PSEA/blob/main/install_r_packages.R
Rscript path/to/install_r_packages.R
rm path/to/install_r_packages.R

Now you are ready to install q2-PSEA. Run the following commands:

pip install git+https://github.com/LadnerLab/q2-PSEA.git

Run qiime info to check for a successful installation. If installation was successful, you should see psea: version in the list of installed plugins.

Using provided example data, average run time for 3 trials was: 1 Minute 21 Seconds

Updating

To update q2-PSEA, run the following command:

pip install -U git+https://github.com/LadnerLab/q2-PSEA.git