README.Rmd

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output: github_document
---

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```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
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  fig.path = "man/figures/README-",
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```

# MotrpacRatTraining6moWAT

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A collection of functions for the analysis and visualization of the MoTrPAC PASS1B white adipose tissue (WAT) data as provided in the <a href="https://motrpac.github.io/MotrpacRatTraining6moData/index.html" target="_blank">MotrpacRatTraining6moData</a> package. This package was built specifically to generate the <a href="https://motrpac.github.io/MotrpacRatTraining6moWATData/index.html" target="_blank">MotrpacRatTraining6moWATData</a> package, so much of it is tailored only for use with those datasets, though users may find some of the functionality contained herein to be useful in other projects:

-   Differential analysis (DA) with the <a href="https://bioconductor.org/packages/release/bioc/html/limma.html" target="_blank">limma</a> and <a href="https://bioconductor.org/packages/release/bioc/html/edgeR.html" target="_blank">edgeR</a> packages
-   Fast Gene Set Enrichment Analysis (FGSEA) with <a href="https://bioconductor.org/packages/release/bioc/html/fgsea.html" target="_blank">fgsea</a> and <a href="https://cran.r-project.org/web/packages/msigdbr/index.html" target="_blank">msigdbr</a>
-   Kinase-Substrate Enrichment Analysis (KSEA) with <a href="https://www.phosphosite.org/homeAction.action">PhosphoSitePlus</a>
-   Over-representation analysis (ORA)
-   Weighted Gene Co-expression Network Analysis (WGCNA)

## Installation

Install this package with `devtools`:

``` r
if (!require("devtools", quietly = TRUE))
  install.packages("devtools")

devtools::install_github("MoTrPAC/MotrpacRatTraining6moWAT")
```

# Preprint

Many, G. M., Sanford, J. A., Sagendorf, T. J., Hou, Z., Nigro, P., Whytock, K., Amar, D., Caputo, T., Gay, N. R., Gaul, D. A., Hirshman, M., Jimenez-Morales, D., Lindholm, M. E., Muehlbauer, M. J., Vamvini, M., Bergman, B., Fernández, F. M., Goodyear, L. J., Ortlund, E. A., ... Schenk, S. (2023). Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue. *BioRxiv*. <a href="https://doi.org/10.1101/2023.02.03.527012" target="_blank">https://doi.org/10.1101/2023.02.03.527012</a>