SPEAQeasy Example Analysis
14 July 2023
1 Analysis
A guided example showing how processed results from the RNAseq pipeline SPEAQeasy can be used in differential expression analyses and visualization. We also show how existing genotype information for a set of samples can be combined with SPEAQeasy results to resolve any identity issues, as can emerge during sequencing.
2 Cite SPEAQeasy
We hope that SPEAQeasy will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
@article {Eagles2021,
author = {Eagles, Nicholas J. and Burke, Emily E. and Leonard, Jacob and Barry, Brianna K. and Stolz, Joshua M. and Huuki, Louise and Phan, BaDoi N. and Larrios Serrato, Violeta and Guti{\'e}rrez-Mill{\'a}n, Everardo and Aguilar-Ordo{\~n}ez, Israel and Jaffe, Andrew E. and Collado-Torres, Leonardo},
title = {SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses},
year = {2021},
doi = {10.1186/s12859-021-04142-3},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://doi.org/10.1186/s12859-021-04142-3},
journal = {BMC Bioinformatics}
}This is a project by the R/Bioconductor-powered Team Data Science at the Lieber Institute for Brain Development.
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3 References
The analysis was possible thanks to R and many of its packages:
- R (R Core Team, 2020)
- BiocStyle (Allaire, Xie, McPherson, Luraschi et al., 2020)
- clusterProfiler (Carlson, 2020)
- devtools (Boettiger, 2021)
- edgeR (Collado-Torres, Nellore, Kammers, Ellis et al., 2017)
- getopt (Collado-Torres, Jaffe, and Burke, 2021)
- here (Davis and Day, 2019)
- limma (Morgan, Obenchain, Hester, and Pagès, 2020)
- jaffelab (Kolde, 2019)
- knitcitations (Müller, 2020)
- org.Hs.eg.db (Neuwirth, 2014)
- pheatmap (Obenchain, Lawrence, Carey, Gogarten et al., 2014)
- RColorBrewer (Oleś, Morgan, and Huber, 2020)
- recount (Ritchie, Phipson, Wu, Hu et al., 2015)
- rmarkdown (Robinson, McCarthy, and Smyth, 2010)
- SummarizedExperiment (Law, Chen, Shi, and Smyth, 2014)
- tidyr (Wickham, Hester, and Chang, 2020)
- VariantAnnotation (Wickham, 2020)
- voom (Yu, Wang, Han, and He, 2012)
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[4] L. Collado-Torres, A. E. Jaffe, and E. E. Burke. jaffelab: Commonly used functions by the Jaffe lab. R package version 0.99.32. 2021. <URL: https://github.com/LieberInstitute/jaffelab>.
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[15] M. E. Ritchie, B. Phipson, D. Wu, Y. Hu, et al. “limma powers differential expression analyses for RNA-sequencing and microarray studies”. In: Nucleic Acids Research 43.7 (2015), p. e47. DOI: 10.1093/nar/gkv007.
[16] M. D. Robinson, D. J. McCarthy, and G. K. Smyth. “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data”. In: Bioinformatics 26.1 (2010), pp. 139-140. DOI: 10.1093/bioinformatics/btp616.
[17] H. Wickham. tidyr: Tidy Messy Data. https://tidyr.tidyverse.org, https://github.com/tidyverse/tidyr. 2020.
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# Time spent creating this report:
diff(c(timestart, Sys.time()))## Time difference of 1.044434 secs# Date this report was generated
message(Sys.time())## 2023-07-14 13:53:34# Reproducibility info
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