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references.bib
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@Book{spatstat-book,
title = {Spatial Point Patterns: Methodology and Applications with
{R}},
author = {Adrian Baddeley and Ege Rubak and Rolf Turner},
year = {2015},
publisher = {Chapman and Hall/CRC Press},
address = {London},
isbn = {9781482210200},
url =
{https://www.routledge.com/Spatial-Point-Patterns-Methodology-and-Applications-with-R/Baddeley-Rubak-Turner/p/book/9781482210200/},
}
@Article{gtsummary,
author = {Daniel D. Sjoberg and Karissa Whiting and Michael Curry and Jessica A. Lavery and Joseph Larmarange},
title = {Reproducible Summary Tables with the gtsummary Package},
journal = {{The R Journal}},
year = {2021},
url = {https://doi.org/10.32614/RJ-2021-053},
doi = {10.32614/RJ-2021-053},
volume = {13},
issue = {1},
pages = {570-580},
}
@Article{modelsummary,
title = {{modelsummary}: Data and Model Summaries in {R}},
author = {Vincent Arel-Bundock},
journal = {Journal of Statistical Software},
year = {2022},
volume = {103},
number = {1},
pages = {1--23},
doi = {10.18637/jss.v103.i01},
}
@article{burkner2017,
title = {{\textbf{brms}}: An {\emph{R}} Package for Bayesian Multilevel Models Using {\emph{Stan}}},
author = {{Bürkner}, Paul-Christian},
year = {2017},
date = {2017},
journal = {Journal of Statistical Software},
volume = {80},
number = {1},
doi = {10.18637/jss.v080.i01},
url = {http://dx.doi.org/10.18637/jss.v080.i01},
langid = {en}
}
@article{brms,
title = {{\textbraceleft}brms{\textbraceright}: An {\textbraceleft}R{\textbraceright} Package for {\textbraceleft}Bayesian{\textbraceright} Multilevel Models Using {\textbraceleft}Stan{\textbraceright}},
author = {{Bürkner}, Paul-Christian},
year = {2017},
date = {2017},
volume = {80},
doi = {10.18637/jss.v080.i01}
}
@article{performance,
title = {{\textbraceleft}performance{\textbraceright}: An {\textbraceleft}R{\textbraceright} Package for Assessment, Comparison and Testing of Statistical Models},
author = {{Lüdecke}, Daniel and Ben-Shachar, Mattan S. and Patil, Indrajeet and Waggoner, Philip and Makowski, Dominique},
year = {2021},
date = {2021},
pages = {3139},
volume = {6},
doi = {10.21105/joss.03139}
}
@article{easystats,
title = {easystats: Framework for Easy Statistical Modeling, Visualization, and Reporting},
author = {{Lüdecke}, Daniel and Ben-Shachar, Mattan S. and Patil, Indrajeet and Wiernik, Brenton M. and Makowski, Dominique},
year = {2022},
date = {2022},
url = {https://easystats.github.io/easystats/}
}
@article{makowski2019,
title = {bayestestR: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework},
author = {Makowski, Dominique and Ben-Shachar, Mattan and {Lüdecke}, Daniel},
year = {2019},
month = {08},
date = {2019-08-13},
journal = {Journal of Open Source Software},
pages = {1541},
volume = {4},
number = {40},
doi = {10.21105/joss.01541},
url = {http://dx.doi.org/10.21105/joss.01541}
}
@article{bayestestR,
title = {bayestestR: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework.},
author = {Makowski, Dominique and Ben-Shachar, Mattan S. and {Lüdecke}, Daniel},
year = {2019},
date = {2019},
pages = {1541},
volume = {4},
doi = {10.21105/joss.01541},
url = {https://joss.theoj.org/papers/10.21105/joss.01541}
}
@article{modelbased,
title = {Estimation of Model-Based Predictions, Contrasts and Means.},
author = {Makowski, Dominique and Ben-Shachar, Mattan S. and Patil, Indrajeet and {Lüdecke}, Daniel},
year = {2020},
date = {2020},
url = {https://github.com/easystats/modelbased}
}
@article{bankhead2017,
title = {QuPath: Open source software for digital pathology image analysis},
author = {Bankhead, Peter and Loughrey, Maurice B. and {Fernández}, {José A.} and Dombrowski, Yvonne and McArt, Darragh G. and Dunne, Philip D. and McQuaid, Stephen and Gray, Ronan T. and Murray, Liam J. and Coleman, Helen G. and James, Jacqueline A. and Salto-Tellez, Manuel and Hamilton, Peter W.},
year = {2017},
month = {12},
date = {2017-12-04},
journal = {Scientific Reports},
volume = {7},
number = {1},
doi = {10.1038/s41598-017-17204-5},
url = {http://dx.doi.org/10.1038/s41598-017-17204-5},
langid = {en}
}
@article{baddeley2005,
title = {{\textbf{spatstat}}: An{\emph{R}}Package for Analyzing Spatial Point Patterns},
author = {Baddeley, Adrian and Turner, Rolf},
year = {2005},
date = {2005},
journal = {Journal of Statistical Software},
volume = {12},
number = {6},
doi = {10.18637/jss.v012.i06},
url = {http://dx.doi.org/10.18637/jss.v012.i06},
langid = {en}
}
@article{spatstat,
title = {Spatial Point Patterns: Methodology and Applications with {\textbraceleft}R{\textbraceright}},
author = {Baddeley, Adrian and Rubak, Ege and Turner, Rolf},
year = {2015},
date = {2015},
url = {https://www.routledge.com/Spatial-Point-Patterns-Methodology-and-Applications-with-R/Baddeley-Rubak-Turner/p/book/9781482210200/}
}
@article{vehtari2016,
title = {Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC},
author = {Vehtari, Aki and Gelman, Andrew and Gabry, Jonah},
year = {2016},
month = {08},
date = {2016-08-30},
journal = {Statistics and Computing},
pages = {1413--1432},
volume = {27},
number = {5},
doi = {10.1007/s11222-016-9696-4},
url = {http://dx.doi.org/10.1007/s11222-016-9696-4},
langid = {en}
}
@article{emmeans,
title = {emmeans: Estimated Marginal Means, aka Least-Squares Means},
author = {Lenth, Russell V.},
year = {2023},
date = {2023},
url = {https://CRAN.R-project.org/package=emmeans}
}
@article{berg2019,
title = {ilastik: interactive machine learning for (bio)image analysis},
author = {Berg, Stuart and Kutra, Dominik and Kroeger, Thorben and Straehle, Christoph N. and Kausler, Bernhard X. and Haubold, Carsten and Schiegg, Martin and Ales, Janez and Beier, Thorsten and Rudy, Markus and Eren, Kemal and Cervantes, Jaime I and Xu, Buote and Beuttenmueller, Fynn and Wolny, Adrian and Zhang, Chong and Koethe, Ullrich and Hamprecht, Fred A. and Kreshuk, Anna},
year = {2019},
month = {09},
date = {2019-09-30},
journal = {Nature Methods},
pages = {1226--1232},
volume = {16},
number = {12},
doi = {10.1038/s41592-019-0582-9},
url = {http://dx.doi.org/10.1038/s41592-019-0582-9},
langid = {en}
}
@article{factoextra,
title = {factoextra: Extract and Visualize the Results of Multivariate Data Analyses},
author = {Kassambara, Alboukadel and Mundt, Fabian},
year = {2020},
date = {2020},
url = {https://CRAN.R-project.org/package=factoextra}
}
@article{burkner2018,
title = {Advanced Bayesian Multilevel Modeling with the R Package brms},
author = {{Bürkner}, Paul-Christian},
year = {2018},
date = {2018},
journal = {The R Journal},
pages = {395},
volume = {10},
number = {1},
doi = {10.32614/rj-2018-017},
url = {http://dx.doi.org/10.32614/RJ-2018-017},
langid = {en}
}
@article{brms,
title = {{\textbraceleft}brms{\textbraceright}: An {\textbraceleft}R{\textbraceright} Package for {\textbraceleft}Bayesian{\textbraceright} Multilevel Models Using {\textbraceleft}Stan{\textbraceright}},
author = {{Bürkner}, Paul-Christian},
year = {2017},
date = {2017},
volume = {80},
doi = {10.18637/jss.v080.i01}
}
@article{berg2019a,
title = {ilastik: interactive machine learning for (bio)image analysis},
author = {Berg, Stuart and Kutra, Dominik and Kroeger, Thorben and Straehle, Christoph N. and Kausler, Bernhard X. and Haubold, Carsten and Schiegg, Martin and Ales, Janez and Beier, Thorsten and Rudy, Markus and Eren, Kemal and Cervantes, Jaime I and Xu, Buote and Beuttenmueller, Fynn and Wolny, Adrian and Zhang, Chong and Koethe, Ullrich and Hamprecht, Fred A. and Kreshuk, Anna},
year = {2019},
month = {09},
date = {2019-09-30},
journal = {Nature Methods},
pages = {1226--1232},
volume = {16},
number = {12},
doi = {10.1038/s41592-019-0582-9},
url = {http://dx.doi.org/10.1038/s41592-019-0582-9},
langid = {en}
}
@article{stirling2021,
title = {CellProfiler 4: improvements in speed, utility and usability},
author = {Stirling, David R. and Swain-Bowden, Madison J. and Lucas, Alice M. and Carpenter, Anne E. and Cimini, Beth A. and Goodman, Allen},
year = {2021},
month = {09},
date = {2021-09-10},
journal = {BMC Bioinformatics},
volume = {22},
number = {1},
doi = {10.1186/s12859-021-04344-9},
url = {http://dx.doi.org/10.1186/s12859-021-04344-9},
langid = {en}
}
@article{carpenter2006,
author = {Carpenter, Anne E and Jones, Thouis R and Lamprecht, Michael R and Clarke, Colin and Kang, In and Friman, Ola and Guertin, David A and Chang, Joo and Lindquist, Robert A and Moffat, Jason and Golland, Polina and Sabatini, David M},
year = {2006},
date = {2006},
journal = {Genome Biology},
pages = {R100},
volume = {7},
number = {10},
doi = {10.1186/gb-2006-7-10-r100},
url = {http://dx.doi.org/10.1186/gb-2006-7-10-r100}
}
@article{spatstat,
title = {Spatial Point Patterns: Methodology and Applications with {\textbraceleft}R{\textbraceright}},
author = {Baddeley, Adrian and Rubak, Ege and Turner, Rolf},
year = {2015},
date = {2015},
url = {https://www.routledge.com/Spatial-Point-Patterns-Methodology-and-Applications-with-R/Baddeley-Rubak-Turner/p/book/9781482210200/}
}
@article{emmeans,
title = {emmeans: Estimated Marginal Means, aka Least-Squares Means},
author = {Lenth, Russell V.},
year = {2023},
date = {2023},
url = {https://CRAN.R-project.org/package=emmeans}
}
@article{schindelin2012,
title = {Fiji: an open-source platform for biological-image analysis},
author = {Schindelin, Johannes and Arganda-Carreras, Ignacio and Frise, Erwin and Kaynig, Verena and Longair, Mark and Pietzsch, Tobias and Preibisch, Stephan and Rueden, Curtis and Saalfeld, Stephan and Schmid, Benjamin and Tinevez, Jean-Yves and White, Daniel James and Hartenstein, Volker and Eliceiri, Kevin and Tomancak, Pavel and Cardona, Albert},
year = {2012},
month = {06},
date = {2012-06-28},
journal = {Nature Methods},
pages = {676--682},
volume = {9},
number = {7},
doi = {10.1038/nmeth.2019},
url = {http://dx.doi.org/10.1038/nmeth.2019},
langid = {en}
}
@article{stirling2021,
title = {CellProfiler 4: improvements in speed, utility and usability},
author = {Stirling, David R. and Swain-Bowden, Madison J. and Lucas, Alice M. and Carpenter, Anne E. and Cimini, Beth A. and Goodman, Allen},
year = {2021},
month = {09},
date = {2021-09-10},
journal = {BMC Bioinformatics},
volume = {22},
number = {1},
doi = {10.1186/s12859-021-04344-9},
url = {http://dx.doi.org/10.1186/s12859-021-04344-9}
}
@article{emmeans,
title = {emmeans: Estimated Marginal Means, aka Least-Squares Means},
author = {Lenth, Russell V.},
year = {2023},
date = {2023},
url = {https://CRAN.R-project.org/package=emmeans}
}
@article{berg2019,
title = {ilastik: interactive machine learning for (bio)image analysis},
author = {Berg, Stuart and Kutra, Dominik and Kroeger, Thorben and Straehle, Christoph N. and Kausler, Bernhard X. and Haubold, Carsten and Schiegg, Martin and Ales, Janez and Beier, Thorsten and Rudy, Markus and Eren, Kemal and Cervantes, Jaime I and Xu, Buote and Beuttenmueller, Fynn and Wolny, Adrian and Zhang, Chong and Koethe, Ullrich and Hamprecht, Fred A. and Kreshuk, Anna},
year = {2019},
month = {09},
date = {2019-09-30},
journal = {Nature Methods},
pages = {1226--1232},
volume = {16},
number = {12},
doi = {10.1038/s41592-019-0582-9},
url = {http://dx.doi.org/10.1038/s41592-019-0582-9},
langid = {en}
}
@article{stirling2021,
title = {CellProfiler 4: improvements in speed, utility and usability},
author = {Stirling, David R. and Swain-Bowden, Madison J. and Lucas, Alice M. and Carpenter, Anne E. and Cimini, Beth A. and Goodman, Allen},
year = {2021},
month = {09},
date = {2021-09-10},
journal = {BMC Bioinformatics},
volume = {22},
number = {1},
doi = {10.1186/s12859-021-04344-9},
url = {http://dx.doi.org/10.1186/s12859-021-04344-9},
langid = {en}
}
@article{bürkner2018,
title = {Advanced Bayesian Multilevel Modeling with the R Package brms},
author = {{Bürkner}, Paul-Christian},
year = {2018},
date = {2018},
journal = {The R Journal},
pages = {395},
volume = {10},
number = {1},
doi = {10.32614/rj-2018-017},
url = {http://dx.doi.org/10.32614/RJ-2018-017},
langid = {en}
}
@article{brms,
title = {{\textbraceleft}brms{\textbraceright}: An {\textbraceleft}R{\textbraceright} Package for {\textbraceleft}Bayesian{\textbraceright} Multilevel Models Using {\textbraceleft}Stan{\textbraceright}},
author = {{Bürkner}, Paul-Christian},
year = {2017},
date = {2017},
volume = {80},
doi = {10.18637/jss.v080.i01}
}
@article{makowski2019,
title = {bayestestR: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework},
author = {Makowski, Dominique and Ben-Shachar, Mattan and {Lüdecke}, Daniel},
year = {2019},
month = {08},
date = {2019-08-13},
journal = {Journal of Open Source Software},
pages = {1541},
volume = {4},
number = {40},
doi = {10.21105/joss.01541},
url = {http://dx.doi.org/10.21105/joss.01541}
}
@article{performance,
title = {{\textbraceleft}performance{\textbraceright}: An {\textbraceleft}R{\textbraceright} Package for Assessment, Comparison and Testing of Statistical Models},
author = {{Lüdecke}, Daniel and Ben-Shachar, Mattan S. and Patil, Indrajeet and Waggoner, Philip and Makowski, Dominique},
year = {2021},
date = {2021},
pages = {3139},
volume = {6},
doi = {10.21105/joss.03139}
}
@article{easystats,
title = {easystats: Framework for Easy Statistical Modeling, Visualization, and Reporting},
author = {{Lüdecke}, Daniel and Ben-Shachar, Mattan S. and Patil, Indrajeet and Wiernik, Brenton M. and Makowski, Dominique},
year = {2022},
date = {2022},
url = {https://easystats.github.io/easystats/}
}
@article{modelsummary-2,
title = {{\textbraceleft}modelsummary{\textbraceright}: Data and Model Summaries in {\textbraceleft}R{\textbraceright}},
author = {Arel-Bundock, Vincent},
year = {2022},
date = {2022},
volume = {103},
doi = {10.18637/jss.v103.i01}
}
@article{gtsummary-2,
title = {Reproducible Summary Tables with the gtsummary Package},
author = {Sjoberg, Daniel D. and Whiting, Karissa and Curry, Michael and Lavery, Jessica A. and Larmarange, Joseph},
year = {2021},
date = {2021},
pages = {570--580},
volume = {13},
doi = {10.32614/RJ-2021-053},
url = {https://doi.org/10.32614/RJ-2021-053}
}
@article{Chandran2021a,
title = {Distinct roles of KLF4 in mesenchymal cell subtypes during lung fibrogenesis},
author = {Chandran, Rachana R. and Xie, Yi and Gallardo-Vara, Eunate and Adams, Taylor and Garcia-Milian, Rolando and Kabir, Inamul and Sheikh, Abdul Q. and Kaminski, Naftali and Martin, Kathleen A. and Herzog, Erica L. and Greif, Daniel M.},
year = {2021},
month = {12},
date = {2021-12-10},
journal = {Nature Communications},
volume = {12},
number = {1},
doi = {10.1038/s41467-021-27499-8},
url = {http://dx.doi.org/10.1038/s41467-021-27499-8},
langid = {en}
}
@article{lofstedt2019,
title = {Gray-level invariant Haralick texture features},
author = {{Löfstedt}, Tommy and Brynolfsson, Patrik and Asklund, Thomas and Nyholm, Tufve and Garpebring, Anders},
editor = {Hatt, Mathieu},
year = {2019},
month = {02},
date = {2019-02-22},
journal = {PLOS ONE},
pages = {e0212110},
volume = {14},
number = {2},
doi = {10.1371/journal.pone.0212110},
url = {http://dx.doi.org/10.1371/journal.pone.0212110},
langid = {en}
}
@article{mahotas,
title = {Mahotas: Open source software for scriptable computer vision},
year = {2013},
month = {07},
date = {2013-07-29},
journal = {Journal of Open Research Software},
pages = {e3},
volume = {1},
number = {1},
doi = {10.5334/jors.ac},
url = {http://dx.doi.org/10.5334/jors.ac},
langid = {en}
}
@article{lê2008,
title = {{\textbf{FactoMineR}}: An{\emph{R}}Package for Multivariate Analysis},
author = {{Lê}, {Sébastien} and Josse, Julie and Husson, {François}},
year = {2008},
date = {2008},
journal = {Journal of Statistical Software},
volume = {25},
number = {1},
doi = {10.18637/jss.v025.i01},
url = {http://dx.doi.org/10.18637/jss.v025.i01},
langid = {en}
}
@article{FactoMineR,
title = {{\textbraceleft}FactoMineR{\textbraceright}: A Package for Multivariate Analysis},
author = {{Lê}, {Sébastien} and Josse, Julie and Husson, {François}},
year = {2008},
date = {2008},
volume = {25},
doi = {10.18637/jss.v025.i01}
}
@article{ggcorrplot,
title = {ggcorrplot: Visualization of a Correlation Matrix using 'ggplot2'},
author = {Kassambara, Alboukadel},
year = {2023},
date = {2023},
url = {https://CRAN.R-project.org/package=ggcorrplot}
}
@article{monaco2016,
title = {flowAI: automatic and interactive anomaly discerning tools for flow cytometry data},
author = {Monaco, Gianni and Chen, Hao and Poidinger, Michael and Chen, Jinmiao and {de Magalhães}, {João Pedro} and Larbi, Anis},
year = {2016},
month = {04},
date = {2016-04-10},
journal = {Bioinformatics},
pages = {2473--2480},
volume = {32},
number = {16},
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