Loading the tidyomics ecosystem

Overview

The tidyomics ecosystem is a set of packages for omics data analysis that work together in harmony; they share common Bioconductor data representations and API design consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command.

The core packages are:

tidyomics_packages()

#   [1] "tidySummarizedExperiment" "tidySingleCellExperiment"
#   [3] "tidyseurat"               "tidybulk"                
#   [5] "plyranges"                "nullranges"              
#   [7] "purrr"                    "rlang"                   
#   [9] "stringr"                  "cli"                     
#  [11] "utils"                    "tidyomics"

The tidyomics ecosystem

You can find out more about each package in the tidyomics ecosystem here:

Package	Intro	GitHub	Description
tidybulk	Vignette	GitHub	Tidy bulk RNA-seq data analysis
tidySummarizedExperiment	Vignette	GitHub	Tidy manipulation of SummarizedExperiment objects
tidySingleCellExperiment	Vignette	GitHub	Tidy manipulation of SingleCellExperiment objects
tidySeurat	Vignette	GitHub	Tidy manipulation of Seurat objects
tidySpatialExperiment	Vignette	GitHub	Tidy manipulation of SpatialExperiment objects
plyranges	Vignette	GitHub	Tidy manipulation of genomics ranges
plyinteractions	Vignette	GitHub	Tidy manipulation of genomic interactions
nullranges	Vignette	GitHub	Generation of null genomic range sets

Installation

Installing the tidyomics package will install all core packages of the tidyomics ecosystem. The tidyomics package can be installed from Bioconductor:

BiocManager::install("tidyomics")

plyinteractions and tidySpatialExperiment are two new packages in the tidyomics ecosystem. plyinteractions and tidySpatialExperiment are both ready to use and are available in Bioconductor. The packages are now reaching maturity and will be added to the core packages for automatic installation mid-2024.

For the time being, plyinteractions and tidySpatialExperiment can be installed independently:

BiocManager::install("plyinteractions")
BiocManager::install("tidySpatialExperiment")

Loading the tidyomics ecosystem

The core tidyomics packages can be attached with:

library(tidyomics)

This command also produces a summary of package versions and function conflicts. Function conflicts are a point of ongoing development and will be addressed over time.

plyinteractions and tidySpatialExperiment can be loaded independently:

library(plyinteractions)
library(tidySpatialExperiment)

You are now ready to start using the tidyomics ecosystem.

sessionInfo()
#  R version 4.4.1 (2024-06-14)
#  Platform: x86_64-pc-linux-gnu
#  Running under: Ubuntu 24.04.1 LTS
#  
#  Matrix products: default
#  BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#  LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#  
#  locale:
#   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
#   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#   [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#  [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#  
#  time zone: Etc/UTC
#  tzcode source: system (glibc)
#  
#  attached base packages:
#  [1] stats     graphics  grDevices utils     datasets  methods   base     
#  
#  loaded via a namespace (and not attached):
#   [1] digest_0.6.37     R6_2.5.1          fastmap_1.2.0     xfun_0.48        
#   [5] tidyomics_1.3.0   magrittr_2.0.3    maketools_1.3.1   glue_1.8.0       
#   [9] cachem_1.1.0      stringr_1.5.1     knitr_1.48        htmltools_0.5.8.1
#  [13] rmarkdown_2.28    buildtools_1.0.0  lifecycle_1.0.4   cli_3.6.3        
#  [17] vctrs_0.6.5       sass_0.4.9        jquerylib_0.1.4   compiler_4.4.1   
#  [21] purrr_1.0.2       sys_3.4.3         tools_4.4.1       evaluate_1.0.1   
#  [25] bslib_0.8.0       yaml_2.3.10       jsonlite_1.8.9    rlang_1.1.4      
#  [29] stringi_1.8.4