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plasmoRUtils

plasmoRUtils enables users to connect to several Plasmodium and other apicomplexan databases via R interface and provides simple functions to carry out other bioinformatics tasks which are non-trival for parasite informatic analysis. For further details, we recommend you read our preprint.

Installation

The easiest way to download package is as follows

pak::pkg_install("Rohit-Satyam/plasmoRUtils", dependencies = TRUE)

If the above method fails, try the following steps:

  1. Before downloading the package, install the following dependencies.
cranpkgs <- c('BiocManager','randomcoloR', 'janitor', 'readr', 'rlang', 'dplyr', 'ggsci', 'rvest',
'easyPubMed', 'plyr', 'scales', 'ggplot2', 'glue', 'tidyr', 'tibble', 'data.table', 'plotly',
'purrr', 'stringr', 'S4Vectors', 'magrittr', 'bio3d', 'httr', 'jsonlite',
'ggpubr', 'gt', 'mgsub', 'reshape2','pathfindR','polyglotr')

install.packages(setdiff(cranpkgs, rownames(installed.packages())), dependencies = TRUE)

biocpkgs <- c("rmarkdown","pRoloc","knitr","BiocStyle","DESeq2","styler","utils","IRanges",
"BiocGenerics","rtracklayer","scuttle","txdbmaker","topGO","drawProteins","GenomicFeatures",
"biomaRt","AnnotationForge","Biostrings","GenomeInfoDb","SingleCellExperiment",
"SingleR","NOISeq","GenomicRanges","BSgenome")

BiocManager::install(setdiff(biocpkgs, rownames(installed.packages())), dependencies = TRUE)
  1. You can install the development version of plasmoRUtils using:
devtools::install_github("Rohit-Satyam/plasmoRUtils")
remotes::install_github('Rohit-Satyam/plasmoRUtils')

Check installation

Once dependencies are installed, the package can be loaded as follows:

# Once installed load the library as
library(plasmoRUtils)

## To re-check if all the dependencies that are required by plasmoRUtils are installed
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

To-do List

  1. Write a wrapper function, easypathFindR, to perform Pathway enrichment analysis quickly.
  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!