Bibliografía#
Vebjorn Ljosa, Katherine L Sokolnicki, and Anne E Carpenter. Annotated high-throughput microscopy image sets for validation. Nat. Methods, 9(7):637, June 2012.
Rebecca A Senft, Barbara Diaz-Rohrer, Pina Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew Gonzales, Peter Bankhead, Edward L Evans, III, Kevin W Eliceiri, and Beth A Cimini. A biologist's guide to planning and performing quantitative bioimaging experiments. PLoS Biol., 21(6):e3002167, June 2023.
Robert Haase, Elnaz Fazeli, David Legland, Michael Doube, Siân Culley, Ilya Belevich, Eija Jokitalo, Martin Schorb, Anna Klemm, and Christian Tischer. A hitchhiker's guide through the bio-image analysis software universe. FEBS Lett., 596(19):2472–2485, October 2022.
Perrine Paul-Gilloteaux, Sébastien Tosi, Jean-Karim Hériché, Alban Gaignard, Hervé Ménager, Raphaël Marée, Volker Baecker, Anna Klemm, Matúš Kalaš, Chong Zhang, Kota Miura, and Julien Colombelli. Bioimage analysis workflows: community resources to navigate through a complex ecosystem. F1000Res., 10:320, April 2021.
James Jonkman, Claire M Brown, Graham D Wright, Kurt I Anderson, and Alison J North. Tutorial: guidance for quantitative confocal microscopy. Nat. Protoc., 15(5):1585–1611, May 2020.
John H. Stockley, Kimberley Evans, Moritz Matthey, Katrin Volbracht, Sylvia Agathou, Jana Mukanowa, Juan Burrone, and Ragnhildur T. Káradóttir. Surpassing light-induced cell damage in vitro with novel cell culture media. Scientific Reports, 7(1):849, Apr 2017. URL: https://doi.org/10.1038/s41598-017-00829-x, doi:10.1038/s41598-017-00829-x.
Zixuan Zhao, Xinyi Chen, Anna M Dowbaj, Aleksandra Sljukic, Kaitlin Bratlie, Luda Lin, Eliza Li Shan Fong, Gowri Manohari Balachander, Zhaowei Chen, Alice Soragni, Meritxell Huch, Yi Arial Zeng, Qun Wang, and Hanry Yu. Organoids. Nature Reviews Methods Primers, 2(1):1–21, December 2022.
Eric C Wait, Michael A Reiche, and Teng-Leong Chew. Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design. J. Cell Sci., November 2020.
Anna Payne-Tobin Jost and Jennifer C Waters. Designing a rigorous microscopy experiment: validating methods and avoiding bias. J. Cell Biol., 218(5):1452–1466, May 2019.
Mathias Uhlen, Anita Bandrowski, Steven Carr, Aled Edwards, Jan Ellenberg, Emma Lundberg, David L Rimm, Henry Rodriguez, Tara Hiltke, Michael Snyder, and Tadashi Yamamoto. A proposal for validation of antibodies. Nat. Methods, 13(10):823–827, October 2016.
Charlotte Stadler, Elton Rexhepaj, Vasanth R. Singan, Robert F. Murphy, Rainer Pepperkok, Mathias Uhlén, Jeremy C. Simpson, and Emma Lundberg. Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells. Nature Methods, 10(4):315–323, Apr 2013. URL: https://doi.org/10.1038/nmeth.2377, doi:10.1038/nmeth.2377.
Méghane Sittewelle, Nuria Ferrandiz, Mary Fesenko, and Stephen J. Royle. Genetically encoded imaging tools for investigating cell dynamics at a glance. Journal of Cell Science, 04 2023. jcs260783. URL: https://doi.org/10.1242/jcs.260783, doi:10.1242/jcs.260783.
Talley J Lambert. FPbase: a community-editable fluorescent protein database. Nat. Methods, 16(4):277–278, April 2019.
Jeremy Sanderson. Fundamentals of microscopy. Curr. Protoc. Mouse Biol., 10(2):e76, June 2020.
Alison J. North. Seeing is believing? A beginners' guide to practical pitfalls in image acquisition . Journal of Cell Biology, 172(1):9–18, 01 2006. URL: https://doi.org/10.1083/jcb.200507103, doi:10.1083/jcb.200507103.
Claire M Brown. Fluorescence microscopy–avoiding the pitfalls. J. Cell Sci., 120(Pt 10):1703–1705, May 2007.
Paula Montero Llopis, Rebecca A Senft, Tim J Ross-Elliott, Ryan Stephansky, Daniel P Keeley, Preman Koshar, Guillermo Marqués, Ya-Sheng Gao, Benjamin R Carlson, Thomas Pengo, Mark A Sanders, Lisa A Cameron, and Michelle S Itano. Best practices and tools for reporting reproducible fluorescence microscopy methods. Nat. Methods, 18(12):1463–1476, December 2021.
Rachel M Lee, Leanna R Eisenman, Satya Khuon, Jesse S Aaron, and Teng-Leong Chew. Believing is seeing - the deceptive influence of bias in quantitative microscopy. J. Cell Sci., January 2024.
Beth A Cimini, Peter Bankhead, Rocco D'Antuono, Elnaz Fazeli, Julia Fernandez-Rodriguez, Caterina Fuster-Barceló, Robert Haase, Helena Klara Jambor, Martin L Jones, Florian Jug, Anna H Klemm, Anna Kreshuk, Stefania Marcotti, Gabriel G Martins, Sara McArdle, Kota Miura, Arrate Muñoz-Barrutia, Laura C Murphy, Michael S Nelson, Simon F Nørrelykke, Perrine Paul-Gilloteaux, Thomas Pengo, Joanna W Pylvänäinen, Lior Pytowski, Arianna Ravera, Annika Reinke, Yousr Rekik, Caterina Strambio-De-Castillia, Daniel Thédié, Virginie Uhlmann, Oliver Umney, Laura Wiggins, and Kevin W Eliceiri. The crucial role of bioimage analysts in scientific research and publication. J. Cell Sci., 137(20):jcs262322, October 2024.
Anne F J Janssen, Sophia Y Breusegem, and Delphine Larrieu. Current methods and pipelines for Image-Based quantitation of nuclear shape and nuclear envelope abnormalities. Cells, January 2022.
Jesse S Aaron, Aaron B Taylor, and Teng-Leong Chew. Image co-localization - co-occurrence versus correlation. J. Cell Sci., February 2018.
Jean-Yves Tinevez, Nick Perry, Johannes Schindelin, Genevieve M Hoopes, Gregory D Reynolds, Emmanuel Laplantine, Sebastian Y Bednarek, Spencer L Shorte, and Kevin W Eliceiri. TrackMate: an open and extensible platform for single-particle tracking. Methods, 115:80–90, February 2017.
Fernanda Garcia-Fossa, Mario Costa Cruz, Marzieh Haghighi, Marcelo Bispo de Jesus, Shantanu Singh, Anne E. Carpenter, and Beth A. Cimini. Interpreting image-based profiles using similarity clustering and single-cell visualization. Current Protocols, 3(3):e713, 2023. URL: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.713, doi:https://doi.org/10.1002/cpz1.713.
Akhila Narla, Brett Kuprel, Kavita Sarin, Roberto Novoa, and Justin Ko. Automated classification of skin lesions: from pixels to practice. J. Invest. Dermatol., 138(10):2108–2110, October 2018.
David R Stirling, Anne E Carpenter, and Beth A Cimini. CellProfiler analyst 3.0: accessible data exploration and machine learning for image analysis. Bioinformatics, 37(21):3992–3994, September 2021.
Philipp Eulenberg, Niklas Köhler, Thomas Blasi, Andrew Filby, Anne E Carpenter, Paul Rees, Fabian J Theis, and F Alexander Wolf. Reconstructing cell cycle and disease progression using deep learning. Nat. Commun., 8(1):463, September 2017.
Juan C Caicedo, Sam Cooper, Florian Heigwer, Scott Warchal, Peng Qiu, Csaba Molnar, Aliaksei S Vasilevich, Joseph D Barry, Harmanjit Singh Bansal, Oren Kraus, Mathias Wawer, Lassi Paavolainen, Markus D Herrmann, Mohammad Rohban, Jane Hung, Holger Hennig, John Concannon, Ian Smith, Paul A Clemons, Shantanu Singh, Paul Rees, Peter Horvath, Roger G Linington, and Anne E Carpenter. Data-analysis strategies for image-based cell profiling. Nat. Methods, 14(9):849–863, August 2017.
Thouis R Jones, Anne E Carpenter, Michael R Lamprecht, Jason Moffat, Serena J Silver, Jennifer K Grenier, Adam B Castoreno, Ulrike S Eggert, David E Root, Polina Golland, and David M Sabatini. Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc. Natl. Acad. Sci. U. S. A., 106(6):1826–1831, February 2009.
Caroline A Schneider, Wayne S Rasband, and Kevin W Eliceiri. NIH image to ImageJ: 25 years of image analysis. Nat. Methods, 9(7):671–675, July 2012.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Daniel James White, Volker Hartenstein, Kevin Eliceiri, Pavel Tomancak, and Albert Cardona. Fiji: an open-source platform for biological-image analysis. Nat. Methods, 9(7):676–682, June 2012.
Curtis T Rueden, Johannes Schindelin, Mark C Hiner, Barry E DeZonia, Alison E Walter, Ellen T Arena, and Kevin W Eliceiri. ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics, 18(1):529, November 2017.
David R Stirling, Madison J Swain-Bowden, Alice M Lucas, Anne E Carpenter, Beth A Cimini, and Allen Goodman. CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics, 22(1):433, September 2021.
Peter Bankhead, Maurice B Loughrey, José A Fernández, Yvonne Dombrowski, Darragh G McArt, Philip D Dunne, Stephen McQuaid, Ronan T Gray, Liam J Murray, Helen G Coleman, Jacqueline A James, Manuel Salto-Tellez, and Peter W Hamilton. QuPath: open source software for digital pathology image analysis. Sci. Rep., 7(1):16878, December 2017.
Fabrice de Chaumont, Stéphane Dallongeville, Nicolas Chenouard, Nicolas Hervé, Sorin Pop, Thomas Provoost, Vannary Meas-Yedid, Praveen Pankajakshan, Timothée Lecomte, Yoann Le Montagner, Thibault Lagache, Alexandre Dufour, and Jean-Christophe Olivo-Marin. Icy: an open bioimage informatics platform for extended reproducible research. Nat. Methods, 9(7):690–696, June 2012.
Ilya Belevich, Merja Joensuu, Darshan Kumar, Helena Vihinen, and Eija Jokitalo. Microscopy image browser: a platform for segmentation and analysis of multidimensional datasets. PLoS Biol., 14(1):e1002340, January 2016.
Nicholas Sofroniew, Talley Lambert, Kira Evans, Juan Nunez-Iglesias, Grzegorz Bokota, Philip Winston, Gonzalo Peña-Castellanos, Kevin Yamauchi, Matthias Bussonnier, Draga Doncila Pop, Ahmet Can Solak, Ziyang Liu, Pam Wadhwa, Alister Burt, Genevieve Buckley, Andrew Sweet, Lukasz Migas, Volker Hilsenstein, Lorenzo Gaifas, Jordão Bragantini, Jaime Rodríguez-Guerra, Hector Muñoz, Jeremy Freeman, Peter Boone, Alan Lowe, Christoph Gohlke, Loic Royer, Andrea Pierré, Hagai Har-Gil, and Abigail McGovern. Napari: a multi-dimensional image viewer for python. November 2022.
Carsen Stringer, Tim Wang, Michalis Michaelos, and Marius Pachitariu. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods, 18(1):100–106, January 2021.
Stuart Berg, Dominik Kutra, Thorben Kroeger, Christoph N Straehle, Bernhard X Kausler, Carsten Haubold, Martin Schiegg, Janez Ales, Thorsten Beier, Markus Rudy, Kemal Eren, Jaime I Cervantes, Buote Xu, Fynn Beuttenmueller, Adrian Wolny, Chong Zhang, Ullrich Koethe, Fred A Hamprecht, and Anna Kreshuk. Ilastik: interactive machine learning for (bio)image analysis. Nat. Methods, 16(12):1226–1232, December 2019.
Levin M Moser, Nodar Gogoberidze, Andréa Papaleo, Alice Lucas, David Dao, Christoph A Friedrich, Lassi Paavolainen, Csaba Molnar, David R Stirling, Jane Hung, Rex Wang, Callum Tromans-Coia, Bin Li, Edward L Evans, Kevin W Eliceiri, Peter Horvath, Anne E Carpenter, and Beth A Cimini. Piximi - an images to discovery web tool for bioimages and beyond. bioRxiv, pages 2024.06.03.597232, June 2024.
Matthew Hartley, Gerard J Kleywegt, Ardan Patwardhan, Ugis Sarkans, Jason R Swedlow, and Alvis Brazma. The BioImage archive - building a home for Life-Sciences microscopy data. J. Mol. Biol., 434(11):167505, June 2022.
Eleanor Williams, Josh Moore, Simon W Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Bálint Antal, Richard K Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E Carazo Salas, and Jason R Swedlow. The image data resource: a bioimage data integration and publication platform. Nat. Methods, 14(8):775–781, August 2017.
Curtis T Rueden, Jeanelle Ackerman, Ellen T Arena, Jan Eglinger, Beth A Cimini, Allen Goodman, Anne E Carpenter, and Kevin W Eliceiri. Scientific community image forum: a discussion forum for scientific image software. PLoS Biol., 17(6):e3000340, June 2019.
Kota Miura, editor. Bioimage Data Analysis. Wiley-VCH, 2016.
Kota Miura and Simon F Nørrelykke. Reproducible image handling and analysis. EMBO J., 40(3):e105889, February 2021.
Siân Culley, Alicia Cuber Caballero, Jemima J Burden, and Virginie Uhlmann. Made to measure: an introduction to quantification in microscopy data. arxiv, February 2023. arXiv:2302.01657.
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary S Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Annette Kopp-Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern Menze, Karel G M Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gaël Varoquaux, and Paul F Jäger. Metrics reloaded: recommendations for image analysis validation. Nat. Methods, 21(2):195–212, February 2024.
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp-Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern Menze, Karel G M Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gaël Varoquaux, Ziv R Yaniv, Paul F Jäger, and Lena Maier-Hein. Understanding metric-related pitfalls in image analysis validation. Nat. Methods, 21(2):182–194, February 2024.
Annika Reinke, Minu D. Tizabi, Carole H. Sudre, Matthias Eisenmann, Tim Rädsch, Michael Baumgartner, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Peter Bankhead, Arriel Benis, Matthew Blaschko, Florian Buettner, M. Jorge Cardoso, Jianxu Chen, Veronika Cheplygina, Evangelia Christodoulou, Beth Cimini, Gary S. Collins, Sandy Engelhardt, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Fred Hamprecht, Daniel A. Hashimoto, Doreen Heckmann-Nötzel, Peter Hirsch, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, A. Emre Kavur, Hannes Kenngott, Jens Kleesiek, Andreas Kleppe, Sven Kohler, Florian Kofler, Annette Kopp-Schneider, Thijs Kooi, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, David Moher, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, M. Alican Noyan, Jens Petersen, Gorkem Polat, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Nicola Rieke, Michael Riegler, Hassan Rivaz, Julio Saez-Rodriguez, Clara I. Sánchez, Julien Schroeter, Anindo Saha, M. Alper Selver, Lalith Sharan, Shravya Shetty, Maarten van Smeden, Bram Stieltjes, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Paul Jäger, and Lena Maier-Hein. Common limitations of image processing metrics: a picture story. 2023. arXiv:2104.05642.
Douglas W Cromey. Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images. Sci. Eng. Ethics, 16(4):639–667, December 2010.
Helena Jambor, Alberto Antonietti, Bradly Alicea, Tracy L Audisio, Susann Auer, Vivek Bhardwaj, Steven J Burgess, Iuliia Ferling, Małgorzata Anna Gazda, Luke H Hoeppner, Vinodh Ilangovan, Hung Lo, Mischa Olson, Salem Yousef Mohamed, Sarvenaz Sarabipour, Aalok Varma, Kaivalya Walavalkar, Erin M Wissink, and Tracey L Weissgerber. Creating clear and informative image-based figures for scientific publications. PLoS Biol., 19(3):e3001161, March 2021.
Kim R M Blenman, Josef Spidlen, David R Parks, Wayne Moore, Adam Treister, Robert Leif, Chris Bray, Michael Goldberg, ISAC Data Standards Task Force, and Ryan Brinkman. ISAC probe tag dictionary: standardized nomenclature for detection and visualization labels used in cytometry and microscopy imaging. Cytometry A, 99(1):103–106, January 2021.
Mee Rie Sheen, Jennifer L Fields, Brian Northan, Judith Lacoste, Lay-Hong Ang, Steven Fiering, and Reproducibility Project: Cancer Biology. Replication study: biomechanical remodeling of the microenvironment by stromal caveolin-1 favors tumor invasion and metastasis. Elife, December 2019.
Guillermo Marqués, Thomas Pengo, and Mark A Sanders. Imaging methods are vastly underreported in biomedical research. Elife, August 2020.
Hong Yu, Shashank Agarwal, Mark Johnston, and Aaron Cohen. Are figure legends sufficient? evaluating the contribution of associated text to biomedical figure comprehension. J. Biomed. Discov. Collab., 4:1, January 2009.
Christopher Schmied, Michael S Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T Carvalho, Catalin Chiritescu, Jana Christopher, Beth A Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G Martins, Aastha Mathur, Kota Miura, Paula Montero Llopis, Roland Nitschke, Alison North, Adam C Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T Scott, Arne Seitz, Olaf Selchow, Ved P Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Douglas Taatjes, Christian Tischer, and Helena Klara Jambor. Community-developed checklists for publishing images and image analyses. Nat. Methods, 21(2):170–181, February 2024.
Jake Lever, Martin Krzywinski, and Naomi Altman. Principal component analysis. Nat. Methods, 14:641–642, July 2017.
Christopher J C Burges. Dimension reduction: a guided tour. Foundations and Trends® in Machine Learning, January 2010.
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Jeffrey T Leek, W Evan Johnson, Hilary S Parker, Andrew E Jaffe, and John D Storey. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics, 28(6):882–883, March 2012.
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