Bibliography

These are the works that the pages of this site cite and that CytePool’s modules cite in their References sections, which help() shows. The groups below say where each is used; the list at the end of the page gives every work in full, with its DOI where it has one. How to cite says which to cite for each function.

Pseudobulk analysis and single-cell studies¶

Cells or samples Squair et al., 2021Zimmerman et al., 2021Murphy & Skene, 2022Junttila et al., 2022Crowell et al., 2020Lun & Marioni, 2017Hafner et al., 2025Nguyen et al., 2023Heumos et al., 2023; studies and atlases Kang et al., 2018Perez et al., 2022Stephenson et al., 2021Yazar et al., 2022Murphy et al., 2023Nakatsuka et al., 2025Garg et al., 2021Srivatsan et al., 2020CZI Cell Science Program et al., 2025Sikkema et al., 2023.

Linear models, empirical Bayes and precision weights¶

limma and its methods Smyth, 2004Smyth et al., 2005Ritchie et al., 2015Phipson et al., 2016McCarthy & Smyth, 2009Lönnstedt & Speed, 2002Law et al., 2014Liu et al., 2015Ritchie et al., 2006Smyth, 2002Smyth, 2025; estimability, leverage and models in R Searle, 1971Hoaglin & Welsch, 1978Wilkinson & Rogers, 1973Chambers & Hastie, 1992Venables et al., 2025R Core Team, 2025Becker et al., 1988.

Counts: normalization, negative binomial models, quasi-likelihood and DESeq2¶

Robinson & Oshlack, 2010Robinson et al., 2010Bullard et al., 2010Anders & Huber, 2010Chen et al., 2016McCarthy et al., 2012Robinson & Smyth, 2008Cox & Reid, 1987Lund et al., 2012Chen et al., 2025Baldoni et al., 2024Phipson, 2013Dunn & Smyth, 2018Love et al., 2014Bourgon et al., 2010Cook, 1977Muzellec et al., 2023Levenberg, 1944Marquardt, 1963

Mixed models and dream¶

Bates et al., 2015Patterson & Thompson, 1971Harville, 1977Henderson, 1975Satterthwaite, 1946Giesbrecht & Burns, 1985Kuznetsova et al., 2017Bertsekas, 1982Hoffman & Schadt, 2016Hoffman & Roussos, 2021Hoffman et al., 2026; Kenward and Roger’s tests and F-tests Kenward & Roger, 1997Halekoh & Højsgaard, 2014Fai & Cornelius, 1996

Gene sets, pathways and interactions¶

Wu et al., 2010Wu & Smyth, 2012Giner & Smyth, 2016Majewski et al., 2010Langsrud, 2005Phipson & Smyth, 2010Goeman & Bühlmann, 2007Barry et al., 2008Subramanian et al., 2005Holland et al., 2020Mompel et al., 2022Liberzon et al., 2015Dimitrov et al., 2022Dimitrov et al., 2024Routledge, 1994Bailey, 1980Hill, 1970Brophy, 1987Zar, 1999

Gene-set files and over-representation analysis GSEA team, 2026Liberzon et al., 2011Young et al., 2010Fisher, 1922Rivals et al., 2007Tavazoie et al., 1999Timmons et al., 2015Wijesooriya et al., 2022Yu et al., 2012.

Composition¶

Phipson et al., 2022Büttner et al., 2021Mangiola et al., 2023Hoffman & Roussos, 2026Dann et al., 2022Yi et al., 2024

Meta-analysis and multiple testing¶

DerSimonian & Laird, 1986Viechtbauer, 2005Viechtbauer, 2010Paule & Mandel, 1982Cochran, 1954Higgins & Thompson, 2002Hartung, 1999Sidik & Jonkman, 2002Knapp & Hartung, 2003Urbut et al., 2019Benjamini & Hochberg, 1995Benjamini & Yekutieli, 2001Holm, 1979Hochberg, 1988Hommel, 1988Simes, 1986

Smoothing, distributions and numerical methods¶

Cleveland, 1979Cleveland, 1981Boor, 1978Hastie, 1992Scott, 1979Freedman & Diaconis, 1981Abramowitz & Stegun, 1964Johnson et al., 1995Olver et al., 2026Wichura, 1988Paulson, 1942Temme, 1979Lentz, 1976Thompson & Barnett, 1986Loader, 2000Mächler, 2012Dekker, 1971Knuth, 1997Ogita et al., 2005Neumaier, 1974Kendall, 1945Golub & Van Loan, 2013Giraud et al., 2005Berrut & Trefethen, 2004Brent, 1973Dowell & Jarratt, 1971Graham, 1969Briggs & Torczon, 1993Goldberg, 1991Hoare, 1961Wirth, 1976

Figures¶

Classical scaling for MDS plots, forest plots, violin plots and the bandwidth of their densities, and the check of the colour palette for colour-vision deficiency Gower, 1966Lewis & Clarke, 2001Hintze & Nelson, 1998Silverman, 1986Machado et al., 2009.

Data structures, file formats and standards¶

Virshup et al., 2024Bredikhin et al., 2022Wolf et al., 2018Heumos et al., 2026Miles et al., 2025Zarr developers, 2023Maitin-Shepard, 2025Deutsch, 1996Deutsch, 1996Collet & Kucherawy, 2021National Institute of Standards and Technology, 2015Yergeau, 2003Bray, 2017IEEE, 2019ISO, 2019