About the Authors
These credits are based on our course contributors table guidelines.
| Credits | Names |
|---|---|
| Pedagogy | |
| Lead Content Instructor | Ava Hoffman |
| Content Idea Contributor | Kasper Hansen |
| Content Directors | Kasper Hansen, Jeff Leek, Frederick Tan |
| Production | |
| Content Publisher | Ira Gooding |
| Technical | |
| Template Publishing Engineers | Candace Savonen, Carrie Wright, Ava Hoffman |
| Publishing Maintenance Engineer | Candace Savonen |
| Technical Publishing Stylists | Carrie Wright, Candace Savonen |
| Package Developers (ottrpal) | John Muschelli, Candace Savonen, Carrie Wright |
| Funding | |
| Funder | National Human Genome Research Institute (NHGRI) |
| Funding Staff | Fallon Bachman, Jennifer Vessio, Emily Voeglein |
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.3 (2022-03-10)
## os Ubuntu 20.04.5 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2023-05-24
## pandoc 2.17.1.1 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## bookdown 0.24 2023-03-22 [1] Github (rstudio/bookdown@88bc4ea)
## bslib 0.3.1 2021-10-06 [1] RSPM (R 4.1.0)
## cachem 1.0.6 2021-08-19 [1] RSPM (R 4.1.0)
## callr 3.7.0 2021-04-20 [1] RSPM (R 4.1.0)
## cli 3.2.0 2022-02-14 [1] RSPM (R 4.1.0)
## crayon 1.5.1 2022-03-26 [1] RSPM (R 4.1.0)
## desc 1.4.1 2022-03-06 [1] RSPM (R 4.1.0)
## devtools 2.4.3 2021-11-30 [1] RSPM (R 4.1.0)
## digest 0.6.29 2021-12-01 [1] RSPM (R 4.1.0)
## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.1.0)
## evaluate 0.15 2022-02-18 [1] RSPM (R 4.1.0)
## fastmap 1.1.0 2021-01-25 [1] RSPM (R 4.1.0)
## fs 1.5.2 2021-12-08 [1] RSPM (R 4.1.0)
## glue 1.6.2 2022-02-24 [1] RSPM (R 4.1.0)
## htmltools 0.5.2 2021-08-25 [1] RSPM (R 4.1.0)
## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.1.0)
## jsonlite 1.8.0 2022-02-22 [1] RSPM (R 4.1.0)
## knitr 1.33 2023-03-22 [1] Github (yihui/knitr@a1052d1)
## lifecycle 1.0.1 2021-09-24 [1] RSPM (R 4.1.0)
## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.1.0)
## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.1.0)
## pkgbuild 1.3.1 2021-12-20 [1] RSPM (R 4.1.0)
## pkgload 1.2.4 2021-11-30 [1] RSPM (R 4.1.0)
## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.1.0)
## processx 3.5.3 2022-03-25 [1] RSPM (R 4.1.0)
## ps 1.6.0 2021-02-28 [1] RSPM (R 4.1.0)
## purrr 0.3.4 2020-04-17 [1] RSPM (R 4.1.0)
## R6 2.5.1 2021-08-19 [1] RSPM (R 4.1.0)
## remotes 2.4.2 2021-11-30 [1] RSPM (R 4.1.0)
## rlang 1.0.2 2023-03-22 [1] Github (r-lib/rlang@34b04a8)
## rmarkdown 2.10 2023-03-22 [1] Github (rstudio/rmarkdown@02d3c25)
## rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.1.3)
## sass 0.4.1 2022-03-23 [1] RSPM (R 4.1.0)
## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.1.0)
## stringi 1.7.6 2021-11-29 [1] RSPM (R 4.1.0)
## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.1.0)
## testthat 3.0.1 2023-03-22 [1] Github (R-lib/testthat@e99155a)
## usethis 2.1.6.9000 2023-03-22 [1] Github (r-lib/usethis@b4b8623)
## withr 2.5.0 2022-03-03 [1] RSPM (R 4.1.0)
## xfun 0.26 2023-03-22 [1] Github (yihui/xfun@74c2a66)
## yaml 2.3.5 2022-02-21 [1] RSPM (R 4.1.0)
##
## [1] /usr/local/lib/R/site-library
## [2] /usr/local/lib/R/library
##
## ──────────────────────────────────────────────────────────────────────────────
Himes, Xiaofeng AND Wagner, Blanca E. AND Jiang. 2014. “RNA-Seq Transcriptome Profiling Identifies Crispld2 as a Glucocorticoid Responsive Gene That Modulates Cytokine Function in Airway Smooth Muscle Cells.” PLOS ONE 9 (6): 1–13. https://doi.org/10.1371/journal.pone.0099625.
Law, CW, K Zeglinski, X Dong, M Alhamdoosh, GK Smyth, and ME Ritchie. 2020. “A Guide to Creating Design Matrices for Gene Expression Experiments.” F1000Research 9 (1444). https://doi.org/10.12688/f1000research.27893.1.
Ritchie, Matthew E., Belinda Phipson, Di Wu, Yifang Hu, Charity W. Law, Wei Shi, and Gordon K. Smyth. 2015. “limma powers differential expression analyses for RNA-sequencing and microarray studies.” Nucleic Acids Research 43 (7): e47–47. https://doi.org/10.1093/nar/gkv007.
Rue-Albrecht, K, F Marini, C Soneson, and ATL Lun. 2018. “iSEE: Interactive SummarizedExperiment Explorer [Version 1; Peer Review: 3 Approved].” F1000Research 7 (741). https://doi.org/10.12688/f1000research.14966.1.
Su, Shian, Charity W Law, Casey Ah-Cann, Marie-Liesse Asselin-Labat, Marnie E Blewitt, and Matthew E Ritchie. 2017. “Glimma: interactive graphics for gene expression analysis.” Bioinformatics 33 (13): 2050–52. https://doi.org/10.1093/bioinformatics/btx094.