omicsTools

The goal of omicsTools is to provide tools for processing and analyzing omics data from genomics, transcriptomics, proteomics, and metabolomics platforms. It provides functions for preprocessing, normalization, visualization, and statistical analysis, as well as machine learning algorithms for predictive modeling. omicsTools is an essential tool for researchers working with high-throughput omics data in fields such as biology, bioinformatics, and medicine.

License: AGPL-3.0

Install dependencies

if (!require("BiocManager", quietly = TRUE)) { install.packages("BiocManager") }
if (!require("pvca", quietly = TRUE)) { BiocManager::install("pvca") }

Installation

CRAN version

You can install the Stable version of omicsTools like so:

install.packages("omicsTools")
#> Installing package into 'C:/Users/bach/AppData/Local/Temp/RtmpqQj0Pu/temp_libpath245079296a59'
#> (as 'lib' is unspecified)
#> package 'omicsTools' successfully unpacked and MD5 sums checked
#> 
#> The downloaded binary packages are in
#>  C:\Users\bach\AppData\Local\Temp\RtmpIN7Pjh\downloaded_packages

Development version

To get a bug fix, or use a feature from the development version, you can install omicsTools from GitHub.

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")
#> 
#> Attaching package: 'devtools'
#> The following object is masked from 'package:BiocManager':
#> 
#>     install

devtools::install_github("omicsTools")
#> Using GitHub PAT from the git credential store.
#> Downloading GitHub repo omicsTools@HEAD
#> rlang  (1.1.3  -> 1.1.4 ) [CRAN]
#> cli    (3.6.2  -> 3.6.3 ) [CRAN]
#> digest (0.6.35 -> 0.6.36) [CRAN]
#> fresh  (0.2.0  -> 0.2.1 ) [CRAN]
#> dbscan (1.1-12 -> 1.2-0 ) [CRAN]
#> Installing 5 packages: rlang, cli, digest, fresh, dbscan
#> Installing packages into 'C:/Users/bach/AppData/Local/Temp/RtmpqQj0Pu/temp_libpath245079296a59'
#> (as 'lib' is unspecified)
#> package 'rlang' successfully unpacked and MD5 sums checked
#> package 'cli' successfully unpacked and MD5 sums checked
#> package 'digest' successfully unpacked and MD5 sums checked
#> package 'fresh' successfully unpacked and MD5 sums checked
#> package 'dbscan' successfully unpacked and MD5 sums checked
#> 
#> The downloaded binary packages are in
#>  C:\Users\bach\AppData\Local\Temp\RtmpIN7Pjh\downloaded_packages
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#>          checking for file 'C:\Users\bach\AppData\Local\Temp\RtmpIN7Pjh\remotes53285a4b5044\omicsTools-baa6316/DESCRIPTION' ...  ✔  checking for file 'C:\Users\bach\AppData\Local\Temp\RtmpIN7Pjh\remotes53285a4b5044\omicsTools-baa6316/DESCRIPTION'
#>       ─  preparing 'omicsTools': (337ms)
#>    checking DESCRIPTION meta-information ...     checking DESCRIPTION meta-information ...   ✔  checking DESCRIPTION meta-information
#>       ─  checking for LF line-endings in source and make files and shell scripts
#>       ─  checking for empty or unneeded directories
#>      Omitted 'LazyData' from DESCRIPTION
#>       ─  building 'omicsTools_1.1.3.tar.gz'
#>      
#> 
#> Installing package into 'C:/Users/bach/AppData/Local/Temp/RtmpqQj0Pu/temp_libpath245079296a59'
#> (as 'lib' is unspecified)

Example of imputation

# Load the CSV data
data_file <- system.file("extdata", "example1.csv", package = "omicsTools")
data <- readr::read_csv(data_file)
#> Rows: 85 Columns: 482
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr   (1): Sample
#> dbl (414): Urea_pos, Lipoamide_pos, AcetylAmino Sugars_pos, Glycerophosphoch...
#> lgl  (67): DBQ_pos.IS, Aminolevulinic Acid_pos, Leucine_pos, Homocystine_pos...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

# Apply the impute function
imputed_data <- omicsTools::handle_missing_values(data)
#> Registered S3 method overwritten by 'GGally':
#>   method from   
#>   +.gg   ggplot2
#> ℹ Starting missing value handling...