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
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', 'echarts4r', 'magrittr', 'bio3d', 'httr', 'jsonlite', 'ggpubr', 'gt', 'mgsub', 'reshape2','pathfindR')
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)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 here
To-do List
- Provide function to access Plasmobase.
- Write wrapper function easypathFindR to quickly perform Pathway enrichment analysis.
- Write 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!