Skip to contents

plasmoRUtils

plasmoRUtils provides an R interface to Plasmodium and other apicomplexan databases, together with utilities for parasite bioinformatics workflows. For further details, we recommend you read our preprint.

Note: Programmatic access to VEuPathDB requires an API key. Set VEUPATHDB_API_KEY in your user .Renviron file before using the authenticated database functions.

Installation

The recommended installation method is:

install.packages("pak") # install pak if necessary
pak::pkg_install("Rohit-Satyam/plasmoRUtils", dependencies = TRUE)

Alternatively, install dependencies and then use the GitHub installer:

  1. Install relevant dependencies:
# nstall CRAN dependencies using CRAN, and Bioconductor dependencies using Bioconductor.
install.packages(c("BiocManager", "remotes"))
BiocManager::install(c("topGO", "biomaRt", "rtracklayer", "GenomicFeatures",
                       "txdbmaker", "AnnotationForge", "SingleR", "SingleCellExperiment",
                       "scuttle", "Biostrings", "pRoloc"), ask = FALSE) 
# The GitHub installer also resolves the package's declared dependencies.
  1. You can install the development version of plasmoRUtils using:
remotes::install_github("Rohit-Satyam/plasmoRUtils", dependencies = TRUE)

Check installation

After installation, load the package as follows:

# Once installed load the library as
library(plasmoRUtils)

## Check and install missing optional dependencies # MODIFIED: this helper can install packages
install_dependencies()

Documentation

The documentation of this package is available at the following:

  1. Introduction to plasmoRUtils
  2. Accessing component databases of VEuPathDB
  3. Other useful functions
  4. RNASeq: Importance of reanalysis
  5. Microarray data reanalysis
  6. Retrieving orthologs

To-do List

  1. Develop an easypathFindR() wrapper for pathway enrichment.
  2. Write a function to make String PPI quickly.

Contributing

We’re excited to have you contribute to this package! If you’d like to help out, try to follow the same style and conventions used in the current functions - where it makes sense, of course. If you have any ideas or suggestions, don’t hesitate to reach out—opening a GitHub issue is usually the best way to start the conversation.

Just a heads up: this project has a Contributor Code of Conduct, so by getting involved, you’re agreeing to play by those rules. Thanks for helping make this project better!