cran: knitr | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: almost 11 years ago

10.12688/f1000research.17824.2

Enhancing gene set enrichment using networks
Cited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago

10.1371/journal.pone.0251194

A computational reproducibility study of PLOS ONE articles featuring longitudinal data analyses
Cited by: 15
Author(s): Heidi Seibold, Severin Czerny, Siona Decke, Roman Dieterle, Thomas Eder, Steffen Fohr, Nico Hahn, Rabea Hartmann, Christoph Heindl, Philipp Kopper, Dario Lepke, Verena Loidl, Maximilian Mandl, Sarah Musiol, Jessica Peter, Alexander Piehler, Elio Rojas, Stefanie Schmid, Hannah Schmidt, Melissa Schmoll, Lennart Schneider, Xiao-Yin To, Viêt Anh Tran, Antje Völker, Moritz Wagner, Joshua Wagner, Maria Waize, Hannah Wecker, Rui Yang, Simone Zellner, Malte Nalenz
Software Mentions: 46
Published: over 3 years ago

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: almost 5 years ago

10.1371/journal.pcbi.1006242

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Cited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Software Mentions: 27
Published: over 6 years ago

10.3390/s20247188

Which Are the Central Aspects of Infant Sleep? The Dynamics of Sleep Composites across Infancy
Cited by: 17
Author(s): Sarah F. Schoch, Reto Huber, Malcolm Kohler, Salomé Kurth
Software Mentions: 26
Published: almost 4 years ago

10.3389/fninf.2013.00052

A framework for streamlining research workflow in neuroscience and psychology
Cited by: 12
Author(s): Jonas Kubilius
Software Mentions: 25
Published: almost 11 years ago

10.1038/s41598-021-96198-7

Cross-modal auditory priors drive the perception of bistable visual stimuli with reliable differences between individuals
Cited by: 2
Author(s): Zsófia Pálffy, Kinga Farkas, Gábor Csukly, Szabolcs Kéri, Bertalan Polner
Software Mentions: 25
Published: over 3 years ago

10.1371/journal.pone.0243927

A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences
Cited by: 13
Author(s): Emine Toparslan, Kemal Karabağ, Uğur Bilge
Software Mentions: 24
Published: almost 4 years ago

10.1037/rev0000169

Simultaneous consonance in music perception and composition.
Cited by: 47
Author(s): Peter M. C. Harrison, Marcus T. Pearce
Software Mentions: 23
Published: over 4 years ago

10.1038/s41396-020-00814-9

Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere
Cited by: 96
Author(s): Robyn J. Wright, Morgan G. I. Langille, Tony R. Walker
Software Mentions: 23
Published: about 4 years ago

10.12688/f1000research.20843.1

Creating and sharing reproducible research code the workflowr way
Cited by: 51
Author(s): John Blischak, Peter Carbonetto, Matthew Stephens
Software Mentions: 22
Published: about 5 years ago

10.3389/fpls.2017.00623

A Practical Guide to Visualization and Statistical Analysis of R. solanacearum Infection Data Using R
Cited by: 25
Author(s): Niklas Schandry
Software Mentions: 21
Published: over 7 years ago

10.1016/j.patter.2021.100322

The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: about 3 years ago

10.1186/s13104-019-4179-2

TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data
Cited by: 75
Author(s): Wei Su, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 20
Published: over 5 years ago

10.3390/s19204551

Assessing Older Adults’ Daily Mobility: A Comparison of GPS-Derived and Self-Reported Mobility Indicators
Cited by: 24
Author(s): Michelle Pasquale Fillekes, Eun Kyeong Kim, Rieke Trumpf, Wiebren Zijlstra, Eleftheria Giannouli, Robert Weibel
Software Mentions: 19
Published: about 5 years ago

10.1371/journal.pone.0061217

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Cited by: 11,386
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 19
Published: over 11 years ago

10.1186/s12859-019-2879-1

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
Cited by: 146
Author(s): Fédérico Marini, Harald Binder
Software Mentions: 18
Published: over 5 years ago

10.1007/s10734-020-00674-4

Lights, camera, active! appreciation of active learning predicts positive attitudes towards lecture capture
Cited by: 6
Author(s): Emily Nordmann, Anne L. Clark, Elliott Spaeth, Jill R D MacKay
Software Mentions: 18
Published: almost 4 years ago

10.1186/s12942-019-0181-0

Towards a comprehensive set of GPS-based indicators reflecting the multidimensional nature of daily mobility for applications in health and aging research
Cited by: 47
Author(s): Michelle Pasquale Fillekes, Eleftheria Giannouli, Eun Kyeong Kim, Wiebren Zijlstra, Robert Weibel
Software Mentions: 18
Published: over 5 years ago

10.1038/s41597-019-0171-x

A multi-omics digital research object for the genetics of sleep regulation
Cited by: 8
Author(s): Jan M, Nastassia Gobet, Shanaz Diessler, Paul Franken, Ioannis Xénarios
Software Mentions: 17
Published: about 5 years ago

10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 17
Published: over 10 years ago

10.1371/journal.pone.0200653

Cryopreservation of human mucosal tissues
Cited by: 13
Author(s): Sean M. Hughes, April L. Ferre, Sarah E Yandura, Cory Shetler, Chris A. R. Baker, Fernanda Calienes, Claire Levy, Rena D. Astronomo, Zhiquan Shu, Gretchen M. Lentz, Michael Fialkow, Anna C. Kirby, M. Juliana McElrath, Elizabeth Sinclair, Lisa C. Rohan, Peter L. Anderson, Barbara L. Shacklett, Charlene S. Dezzutti, Dayong Gao, Florian Hladik
Software Mentions: 17
Published: over 6 years ago

10.1186/s12859-020-03819-5

ideal: an R/Bioconductor package for interactive differential expression analysis
Cited by: 18
Author(s): Fédérico Marini, Jan Linke, Harald Binder
Software Mentions: 17
Published: almost 4 years ago

10.1128/MRA.00129-19

omu, a Metabolomics Count Data Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Cited by: 12
Author(s): Connor R. Tiffany, Andreas J. Bäumler
Software Mentions: 16
Published: over 5 years ago

10.1016/j.xpro.2021.100768

A computational approach for identification of core modules from a co-expression network and GWAS data
Cited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: about 3 years ago

10.1080/17453674.2020.1846956

Uncemented or cemented stems in first-time revision total hip replacement? An observational study of 867 patients including assessment of femoral bone defect size
Cited by: 7
Author(s): Yosef Tyson, Christer Hillman, Norbert Majenburg, Olof Sköldenberg, Ola Rolfson, Johan Kärrholm, Maziar Mohaddes, Nils P Hailer
Software Mentions: 16
Published: about 4 years ago

10.1371/journal.pone.0231982

Rapid processing of neutral and angry expressions within ongoing facial stimulus streams: Is it all about isolated facial features?
Cited by: 2
Author(s): Antonio Schettino, Emanuele Porcu, Christopher Gundlach, Christian Keitel, Matthias Müller
Software Mentions: 16
Published: over 4 years ago

10.1371/journal.pgen.1008927

On the cross-population generalizability of gene expression prediction models
Cited by: 34
Author(s): Kevin L. Keys, Angel C. Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. LeNoir, Jimmie C. Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard, Christopher R. Gignoux
Software Mentions: 16
Published: over 4 years ago

10.3389/fneur.2019.01366

Prediction of Early TBI Mortality Using a Machine Learning Approach in a LMIC Population
Cited by: 39
Author(s): Robson Luís Oliveira de Amorim, Louise Makarem Oliveira, Luis Marcelo Malbouisson, Márcia Mitie Nagumo, Marcela Simoes, Leandro Miranda, Edson Bor‐Seng‐Shu, André Beer‐Furlan, Almir Ferreira de Andrade, Andrés M. Rubiano, Manoel Jacobsen Teixeira, Angelos G. Kolias, Wellingson Silva Paiva
Software Mentions: 15
Published: almost 5 years ago

10.1128/mBio.02120-17

Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients
Cited by: 95
Author(s): Matthew K. Doherty, Tao Ding, Charlie C. Koumpouras, Shannon Telesco, Calixte S. Monast, Anuk Das, Carrie Brodmerkel, Patrick D. Schloss
Software Mentions: 15
Published: over 6 years ago

10.12688/f1000research.8987.2

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Cited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 years ago

10.3390/genes12071044

CircIMPACT: An R Package to Explore Circular RNA Impact on Gene Expression and Pathways
Cited by: 3
Author(s): Alessia Buratin, Enrico Gaffo, Anna Dal Molin, Stefania Bortoluzzi
Software Mentions: 15
Published: over 3 years ago

10.1523/ENEURO.0328-20.2020

Group II Metabotropic Glutamate Receptors Modulate Sound Evoked and Spontaneous Activity in the Mouse Inferior Colliculus
Cited by: 1
Author(s): Inga Kristaponyte, Nichole L. Beebe, Jesse W. Young, Sharad J. Shanbhag, Brett R. Schofield, Alexander V. Galazyuk
Software Mentions: 14
Published: almost 4 years ago

10.1186/s12859-021-03970-7

stochprofML: stochastic profiling using maximum likelihood estimation in R
Cited by: 3
Author(s): Lisa Amrhein, Christiane Fuchs
Software Mentions: 14
Published: over 3 years ago

10.7717/peerj.4729

Effects of nettle slurry (Urtica dioica L.) used as foliar fertilizer on potato (Solanum tuberosum L.) yield and plant growth
Cited by: 9
Author(s): Alfonso Garmendia, María Dolores Raigón, Olmo Marques, M. Ferriol, Jorge Royo, Hugo Merlé
Software Mentions: 14
Published: over 6 years ago

10.1371/journal.pone.0218310

Evaluating health facility access using Bayesian spatial models and location analysis methods
Cited by: 8
Author(s): Nicholas Tierney, Antonietta Mira, H Reinhold, Giuseppe Arbia, Samuel Clifford, Angelo Auricchio, Tiziano Moccetti, Stefano Peluso, Kerrie Mengersen
Software Mentions: 14
Published: over 5 years ago

10.1038/s41598-020-76843-3

Analyzing long-term impacts of ungulate herbivory on forest-recruitment dynamics at community and species level contrasting tree densities versus maximum heights
Cited by: 10
Author(s): Ursula Nopp‐Mayr, Susanne Reimoser, Friedrich Reimoser, Frederik Sachser, Leopold Obermair, Georg Gratzer
Software Mentions: 14
Published: about 4 years ago

10.1371/journal.pone.0206563

Nitrogen addition pulse has minimal effect in big sagebrush (Artemisia tridentata) communities on the Pinedale Anticline, Wyoming (USA)
Cited by: 1
Author(s): Christopher W. Beltz, Megan L. Mobley, Ingrid C. Burke
Software Mentions: 13
Published: over 5 years ago

10.12688/f1000research.6379.2

regionReport: Interactive reports for region-level and feature-level genomic analyses
Cited by: 2
Author(s): Leonardo Collado‐Torres, Andrew E. Jaffe, Jeffrey T. Leek
Software Mentions: 13
Published: over 8 years ago

10.1099/mgen.0.000583

rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data
Cited by: 5
Author(s): Ivan Sserwadda, Gerald Mboowa
Software Mentions: 13
Published: over 3 years ago

10.1186/s12859-020-03922-7

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
Cited by: 3
Author(s): Krutika S. Gaonkar, Fédérico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam Resnick, Konstantin Strauch, Jaclyn N. Taroni, Jo Lynne Rokita
Software Mentions: 13
Published: almost 4 years ago

10.1200/PO.20.00158

Breakthrough Cancer Pain Clinical Features and Differential Opioids Response: A Machine Learning Approach in Patients With Cancer From the IOPS-MS Study
Cited by: 9
Author(s): Francesco Pantano, Tea Zeppola, Angelo Onorato, Michele Iuliani, Sonia Simonetti, Bruno Vincenzi, Daniele Santini, Sebastiano Mercadante, Paolo Marchetti, Arturo Cuomo, Augusto Caraceni, Rocco Domenico Mediati, Renato Vellucci, Massimo Mammucari, Silvia Natoli, Marzia Lazzari, Mario Dauri, Claudio Adile, Mario Airoldi, Giuseppe Azzarello, Livio Blasi, Bruno Chiurazzi, Daniela Degiovanni, Flavio Fusco, Vittorio Guardamagna, Simeone Liguori, Liana Palermo, Sergio Mameli, Francesco Masedu, Teresita Mazzei, Rita Maria Melotti, Valentino Menardo, Danilo Miotti, S. Moroso, Gaetano Pascoletti, Stefano De Santis, Remo Orsetti, Alfonso Papa, Sergio Ricci, E. Scelzi, Michele Sofia, Federica Aielli, Alessandro Valle, Giuseppe Tonini
Software Mentions: 12
Published: about 4 years ago

10.1186/s12998-019-0261-z

Concurrent validity of lower extremity kinematics and jump characteristics captured in pre-school children by a markerless 3D motion capture system
Cited by: 23
Author(s): Steen Harsted, Anders Holsgaard-Larsen, Lise Hestbæk, Eleanor Boyle, Henrik Hein Lauridsen
Software Mentions: 12
Published: over 5 years ago

10.1371/journal.pone.0243295

Polish is quantitatively different on quartzite flakes used on different worked materials
Cited by: 12
Author(s): Antonella Pedergnana, Ivan Calandra, Adrian Evans, Konstantin Bob, Andreas Hildebrandt, Andreu Ollé
Software Mentions: 12
Published: almost 4 years ago

10.1093/gigascience/giab011

The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets
Cited by: 2
Author(s): Holly C. Beale, Jacquelyn Roger, Matthew Cattle, Liam T. McKay, Drew Thompson, Katrina Learned, A. Geoffrey Lyle, Ellen Kephart, R. Currie, Du Linh Lam, Lauren Sanders, Jacob Pfeil, John Vivian, Isabel Bjork, Sofie R. Salama, David Haussler, Olena M. Vaske
Software Mentions: 12
Published: over 3 years ago

10.12688/f1000research.27893.1

A guide to creating design matrices for gene expression experiments
Cited by: 18
Author(s): Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 12
Published: almost 4 years ago

10.1371/journal.pone.0156293

Cryopreservation of Human Mucosal Leukocytes
Cited by: 14
Author(s): Sean M. Hughes, Zhiquan Shu, Claire Levy, April L. Ferre, Heather Hartig, Cifeng Fang, Gretchen M. Lentz, Michael Fialkow, Anna C. Kirby, Kristina M. Adams Waldorf, Ronald S. Veazey, Anja Germann, Hagen von Briesen, M. Juliana McElrath, Charlene S. Dezzutti, Elizabeth Sinclair, Chris A. R. Baker, Barbara L. Shacklett, Dayong Gao, Florian Hladik
Software Mentions: 12
Published: over 8 years ago

10.1167/jov.21.1.1

Flexible contextual modulation of naturalistic texture perception in peripheral vision
Cited by: 9
Author(s): Daniel Herrera-Esposito, Ruben Coen-Cagli, Leonel Gómez-Sena
Software Mentions: 11
Published: almost 4 years ago

10.7717/peerj.4152

Population structure and phenotypic variation ofSclerotinia sclerotiorumfrom dry bean (Phaseolus vulgaris) in the United States
Cited by: 28
Author(s): Zhian N. Kamvar, Bimal S. Amaradasa, Rachana Jhala, Serena McCoy, James R. Steadman, Sydney E. Everhart
Software Mentions: 11
Published: almost 7 years ago

10.1371/journal.pone.0132783

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities
Cited by: 388
Author(s): Mads Albertsen, Søren Michael Karst, Anja Ziegler, Rasmus Hansen Kirkegaard, Per Halkjær Nielsen
Software Mentions: 11
Published: over 9 years ago

10.3389/fmolb.2021.635074

Decoding Neuromuscular Disorders Using Phenotypic Clusters Obtained From Co-Occurrence Networks
Cited by: 3
Author(s): Elena Díaz-Santiago, M. Gonzalo Claros, Raquel Yahyaoui, Yolanda de Diego-Otero, Rocío Velasco Calvo, Janet Hoenicka, Francesc Palau, Juan A. G. Ranea, James R. Perkins
Software Mentions: 11
Published: over 3 years ago

10.1186/s12913-021-06509-x

Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England
Cited by: 20
Author(s): Quentin J. Leclerc, Naomi M. Fuller, Ruth H. Keogh, Karla Díaz-Ordaz, Richard Sekula, Malcolm G Semple, J Kenneth Baillie, Malcolm G Semple, Peter Openshaw, Gail Carson, Beatrice Alex, Benjamin Bach, Wendy S. Barclay, Debby Bogaert, Meera Chand, Graham Cooke, Annemarie B Docherty, Jake Dunning, Ana da Silva Filipe, Tom Fletcher, Christopher Green, Ewen M Harrison, Julian A. Hiscox, Antonia Ho, Peter Horby, Samreen Ijaz, Saye Khoo, Paul Klenerman, Andrew Law, Wei Shen Lim, Alexander J. Mentzer, Laura Merson, Alison Meynert, Mahdad Noursadeghi, Shona C. Moore, Massimo Palmarini, William A. Paxton, Georgios Pollakis, Nicholas Price, Andrew Rambaut, David L. Robertson, Clark D Russell, Vanessa Sancho‐Shimizu, Janet T. Scott, Thushan I. de Silva, Louise Sigfrid, Tom Solomon, Shiranee Sriskandan, D.I. Stuart, Charlotte Summers, Richard S. Tedder, Emma C. Thomson, A. A. Roger Thompson, Ryan S. Thwaites, Lance Turtle, Maria Zambon, Hayley Hardwick, Chloe Donohue, Ruth Lyons, Fiona Griffiths, Wilna Oosthuyzen, Lisa Norman, Riinu Pius, Tom Drake, Cameron J Fairfield, Stephen R Knight, Kenneth A McLean, Derek Murphy, Catherine Shaw, Jo Ann Dalton, James Lee, Daniel Plotkin, Michelle Girvan, Eglė Savičiūtė, Stephanie Roberts, Janet Harrison, Laura Marsh, Marie Connor, Sophie Halpin, Clare Jackson, Carrol Gamble, Claire Petersen, Scott Mullaney, Gary Leeming, Murray Wham, Sara Clohisey, Ross Hendry, James Scott-Brown, William Greenhalf, Victoria Shaw, Sarah E. McDonald, Seán Keating, Katie A. Ahmed, J. A. Armstrong, Milton Ashworth, Innocent G Asiimwe, Siddharth Bakshi, Samantha L. Barlow, Laura Booth, Benjamin Brennan, Katie Bullock, Benjamin W. A. Catterall, Jordan Clark, Emily Clarke, Sarah Cole, Louise Cooper, Helen Cox, Christopher Davis, Oslem Dincarslan, Chris Dunn, Philip Dyer, Angela Elliott, Anthony Evans, Lorna Finch, L. W. Fisher, Terry Foster, Isabel García-Dorival, Philip Gunning, Catherine Hartley, Antonia Ho, Rebecca L. Jensen, Christopher B. Jones, Trevor R. Jones, Shadia Khandaker, Katharine King, Robyn T. Kiy, Chrysa Koukorava, Annette Lake, Suzannah Lant, Diane Latawiec, Lara Lavelle-Langham, Daniella Lefteri, Lauren Lett, Lucia A Livoti, Maria Elisabetta Mancini, Sarah E. McDonald, Laurence McEvoy, John McLauchlan, Soeren Metelmann, Nahida S. Miah, Joanna Middleton, Joyce M. Mitchell, Ellen Murphy, Rebekah Penrice-Randal, Jack Pilgrim, Tessa Prince, Will Reynolds, Paul Ridley, Debby Sales, Victoria Shaw, Rebecca K. Shears, Benjamin Small, Krishanthi Subramaniam, Agnieska Szemiel, Aislynn Taggart, Jolanta Tanianis-Hughes, Jordan Thomas, Erwan Trochu, Libby van Tonder, Eve Wilcock, J. Eunice Zhang, Kayode Adeniji, Daniel Agranoff, Ken Agwuh, Dhiraj Ail, Ana Alegria, Brian Angus, Abdul Ashish, D. Atkinson, Shahedal Bari, Gavin Barlow, Stella Barnass, Nicholas Barrett, Christopher Bassford, David Baxter, Michael Beadsworth, Jolanta Bernatoniene, John C. Berridge, Nicola Best, Pieter Bothma, David Brealey, Robin Brittain-Long, Naomi Bulteel, Tom Burden, Andrew Burtenshaw, Vikki Caruth, David Chadwick, Duncan Chambler, Nigel Chee, Jenny Child, Srikanth Chukkambotla, Tom Clark, Paul Collini, Catherine Cosgrove, Jason Cupitt, Maria-Teresa Cutino-Moguel, Paul Dark, Chris Dawson, Samir Dervisevic, Phil Donnison, Sam Douthwaite, Ingrid DuRand, Ahilanadan Dushianthan, Tristan Dyer, Cariad Evans, Alice C Eziefula, Chrisopher Fegan, Adam Finn, Duncan Fullerton, Sanjeev Garg, Sanjeev Garg, Atul Garg, Effrossyni Gkrania‐Klotsas, Jo Godden, Arthur R. Goldsmith, Clive Graham, Elaine Hardy, Stuart Hartshorn, Daniel Harvey, Peter Havalda, Daniel B. Hawcutt, Maria Hobrok, Luke Hodgson, Anil Hormis, Michael Jacobs, Susan Jain, Paul Jennings, Agilan Kaliappan, Vidya Kasipandian, Stephen Kegg, M.C. Kelsey, Jason Kendall, Caroline Kerrison, Ian Kerslake, Oliver Koch, Gouri Koduri, George Koshy, Shondipon Laha, Steven Laird, Susan Larkin, Tamás Leiner, Patrick Lillie, James Limb, Vanessa Linnett, Jeff Little, Michael MacMahon, Emily Macnaughton, Ravish Mankregod, Huw Masson, Elijah Matovu, Katherine McCullough, Ruth McEwen, Manjula Meda, Gary L. Mills, Jane Minton, Mariyam Mirfenderesky, Kavya Mohandas, Quen Mok, James Moon, Elinoor Moore, Patrick Morgan, Craig C. Morris, Katherine Mortimore, Samuel Moses, Mbiye Mpenge, Rohinton Mulla, Michael V. Murphy, Megan Nagel, Thapas Nagarajan, Mark Nelson, Igor Otahal, Mark Pais, Selva Panchatsharam, Hassan Paraiso, Brij Patel, Natalie Pattison, Justin Pepperell, Mark Peters, Mandeep Phull, Stefania Pintus, Jagtur Singh Pooni, Frank A. Post, David J. Price, Rachel Prout, Nikolas Rae, Henrik Reschreiter, Tim Reynolds, Neil Richardson, Mark Roberts, Devender Roberts, Alistair Rose, Guy Rousseau, Brendan Ryan, Taranprit Saluja, Aarti Shah, Prad Shanmuga, Anil Sharma, Anna Shawcross, Jeremy Sizer, Manu Shankar-Hari, Richard Smith, Catherine Snelson, Nick Spittle, Nikki Staines, Tom Stambach, Richard Stewart, Pradeep Subudhi, Tamás Szakmány, Kate Tatham, Thomas Jo, Chris Thompson, Robert J. Thompson, Ascanio Tridente, Darell Tupper-Carey, Mary Twagira, Andrew Ustianowski, Nick Vallotton, Lisa Vincent-Smith, Shico Visuvanathan, Alan Vuylsteke, Sam Waddy, Rachel Wake, Andrew Walden, Ingeborg Welters, Tony Whitehouse, Paul Whittaker, Ashley Whittington, Meme Wijesinghe, Martin Williams, Lawrence A. Wilson, Sarah Wilson, Stephen Winchester, Martin Wiselka, Adam Wolverson, Daniel G. Wooton, Andrew Workman, Bryan Yates, Peter Young, Matthew Quaife, Christopher Jarvis, Sophie Meakin, Billy J Quilty, Kiesha Prem, C. Julian Villabona-Arenas, Fiona Yueqian Sun, Kaja Abbas, Megan Auzenbergs, Amy Gimma, Damien C. Tully, Katharine Sherratt, Alicia Roselló, Nicholas Davies, Yang Liu, Rachel Lowe, Hamish Gibbs, Naomi R. Waterlow, W. John Edmunds, David Simons, Graham Medley, James D. Munday, Stefan Flasche, Frank Sandmann, Alicia Showering, Rosalind M Eggo, Yung-Wai Desmond Chan, Carl A. B. Pearson, Adam J. Kucharski, Anna M Foss, Timothy Russell, Nikos I. Bosse, Mark Jit, Sam Abbott, Jack Williams, Akira Endo, Samuel Clifford, Georgia R. Gore-Langton, Petra Klepac, Oliver J. Brady, Joel Hellewell, Sebastian Funk, Kevin van Zandvoort, Rosanna C. Barnard, Emily Nightingale, Thibaut Jombart, Katherine E. Atkins, Simon R. Procter, Gwenan M. Knight
Software Mentions: 11
Published: over 3 years ago

10.3389/fpsyg.2021.545268

Beholden: The Emotional Effects of Having Eye Contact While Breaking Social Norms
Cited by: 2
Author(s): Ranjit K. Singh, Birgit J. Voggeser, Anja S. Göritz
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0178895

Familiarity facilitates feature-based face processing
Cited by: 18
Author(s): Matteo Visconti di Oleggio Castello, Kelsey G. Wheeler, Carlo Cipolli, M. Ida Gobbini
Software Mentions: 10
Published: over 7 years ago

10.1186/s12859-016-1125-3

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis
Cited by: 3
Author(s): Nathan James Allen Cormier, Tyler Kolisnik, Mark Bieda
Software Mentions: 10
Published: over 8 years ago

10.1186/s12940-021-00693-3

Examining the role of wind in human illness due to pesticide drift in Washington state, 2000–2015
Cited by: 3
Author(s): Edward J. Kasner, Joanne Bonnar Prado, Michael G. Yost, Richard A. Fenske
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-017-09303-0

The impact of immigration on microbial community composition in full-scale anaerobic digesters
Cited by: 111
Author(s): Rasmus Hansen Kirkegaard, Simon Jon McIlroy, Jannie Munk Kristensen, Marta Nierychlo, Søren Michael Karst, Morten Simonsen Dueholm, Mads Albertsen, Per Halkjær Nielsen
Software Mentions: 10
Published: about 7 years ago

10.1371/journal.pone.0218773

Demand and level of service inflation in Floating Catchment Area (FCA) methods
Cited by: 34
Author(s): Antonio Páez, Christopher D. Higgins, Salvatore Vivona
Software Mentions: 10
Published: over 5 years ago

10.1186/s12936-020-3133-z

Influence of house characteristics on mosquito distribution and malaria transmission in the city of Yaoundé, Cameroon
Cited by: 10
Author(s): Carmène Sandra Ngadjeu, Patricia Doumbe-Belisse, Abdou Talipouo, Landre Djamouko-Djonkam, Parfait Awono-Ambene, Sévilor Kekeunou, Wilson Toussile, Charles S. Wondji, Christophe Antonio-Nkondjio
Software Mentions: 9
Published: almost 5 years ago

10.1128/mSphere.00097-18

Influential Parameters for the Analysis of Intracellular Parasite Metabolomics
Cited by: 11
Author(s): Maureen A. Carey, Vincent Covelli, Audrey C. Brown, Gregory L. Medlock, Mareike Haaren, Jessica G. Cooper, Jason A. Papin, Jennifer L. Guler
Software Mentions: 9
Published: over 6 years ago

10.1186/s12859-019-2799-0

FastqPuri: high-performance preprocessing of RNA-seq data
Cited by: 22
Author(s): Paula Pérez-Rubio, Claudio Lottaz, Julia C. Engelmann
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0193164

Mosquito pornoscopy: Observation and interruption of Aedes aegypti copulation to determine female polyandric event and mixed progeny
Cited by: 10
Author(s): Danilo O. Carvalho, Samira Chuffi, Rafaella Sayuri Ioshino, I. C. S. Marques, Regina Fini, Maria Karina Costa, Helena Rocha Corrêa de Araújo, André Luis Costa-da-Silva, Bianca Burini Kojin, Margareth Lara Capurro
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0190195

Additional statistical and graphical methods for analyzing site formation processes using artifact orientations
Cited by: 39
Author(s): Shannon P. McPherron
Software Mentions: 9
Published: almost 7 years ago

10.1038/s41598-018-31780-0

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome
Cited by: 67
Author(s): Anne Skakkebæk, Morten Muhlig Nielsen, Christian Trolle, Søren Vang, Henrik Hornshøj, Jakob Hedegaard, Mikkel Wallentin, Anders Bojesen, Jens Michael Hertz, Jens Fedder, John R. Østergaard, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-018-30701-5

Electrophysiological correlates of the interplay between low-level visual features and emotional content during word reading
Cited by: 22
Author(s): Sebastian Schindler, Antonio Schettino, Gilles Pourtois
Software Mentions: 9
Published: over 6 years ago

10.1016/j.dib.2020.106651

Impact of malnutrition on survival in adult patients after elective cardiac surgery: Long-term follow up data
Cited by: 0
Author(s): Sergey Efremov, Tatiana Ionova, Tatiana Nikitina, Pavel E. Vedernikov, Timur Dzhumatov, Timofey S. Ovchinnikov, Abduvahhob A. Rashidov, Alexandr E Khomenko, Christian Stoppe, Daren K. Heyland, В. В. Ломиворотов
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12859-017-1651-7

Zipper plot: visualizing transcriptional activity of genomic regions
Cited by: 5
Author(s): Francisco Avila Cobos, Jasper Anckaert, Pieter-Jan Volders, Celine Everaert, Dries Rombaut, Jo Vandesompele, Katleen De Preter, Pieter Mestdagh
Software Mentions: 9
Published: over 7 years ago

10.1371/journal.pone.0244122

Easyreporting simplifies the implementation of Reproducible Research layers in R software
Cited by: 0
Author(s): Dario Righelli, Claudia Angelini
Software Mentions: 8
Published: over 3 years ago

10.1161/HYPERTENSIONAHA.121.17403

Blood Pressure Determinants of Cerebral White Matter Hyperintensities and Microstructural Injury: UK Biobank Cohort Study
Cited by: 13
Author(s): Karolina Wartolowska, Alastair Webb
Software Mentions: 8
Published: over 3 years ago

10.3390/metabo11070463

Sex-Specific Relationship between the Cardiorespiratory Fitness and Plasma Metabolite Patterns in Healthy Humans—Results of the KarMeN Study
Cited by: 5
Author(s): Sina Kistner, Maik Döring, Ralf Krüger, M Rist, Christoph H. Weinert, Diana Bunzel, Benedikt Merz, Katrin Radloff, Rainer Neumann, Sascha Härtel, Achim Bub
Software Mentions: 8
Published: over 3 years ago

10.12688/wellcomeopenres.15210.2

"If you catch my drift...": ability to infer implied meaning is distinct from vocabulary and grammar skills
Cited by: 10
Author(s): Alexander C. Wilson, Dorothy V. M. Bishop
Software Mentions: 8
Published: over 5 years ago

10.3758/s13428-019-01236-y

formr: A study framework allowing for automated feedback generation and complex longitudinal experience-sampling studies using R
Cited by: 120
Author(s): Rana Arslan, Matthias P. Walther, Cyril Tata
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0211196

Myopia is associated with education: Results from NHANES 1999-2008
Cited by: 31
Author(s): Stefan Nickels, Susanne Hopf, Norbert Pfeiffer, Alexander K. Schuster
Software Mentions: 8
Published: almost 6 years ago

10.3390/jintelligence6030041

How Specific Abilities Might Throw ‘g’ a Curve: An Idea on How to Capitalize on the Predictive Validity of Specific Cognitive Abilities
Cited by: 4
Author(s): Matthias Ziegler, Aaron Peikert
Software Mentions: 8
Published: about 6 years ago

10.1093/eurheartj/ehaa756

Midlife blood pressure is associated with the severity of white matter hyperintensities: analysis of the UK Biobank cohort study
Cited by: 56
Author(s): Karolina Wartolowska, Alastair Webb
Software Mentions: 8
Published: almost 4 years ago

10.1186/s13059-015-0675-4

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer
Cited by: 42
Author(s): Eunsun Oh, Stephen M Christensen, Sindhu Ghanta, Jong Cheol Jeong, Octavian Bucur, Benjamin Glass, Laleh Montaser‐Kouhsari, Nicholas W. Knoblauch, Nicholas Bertos, Sadiq M.I. Saleh, Benjamin Haibe‐Kains, Morag Park, Andrew H. Beck
Software Mentions: 7
Published: over 9 years ago

10.1186/s12859-021-04233-1

BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes
Cited by: 2
Author(s): Yasmine Mansour, Annie Château, Anna-Sophie Fiston-Lavier
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0233309

Short Report: Asymptomatic Zika virus infections with low viral loads not likely to establish transmission in New Orleans Aedes populations
Cited by: 0
Author(s): Matthew J. Ward, Brendan H Carter, Christine Walsh, Joshua Yukich, Dawn M. Wesson, Rebecca C. Christofferson
Software Mentions: 7
Published: over 4 years ago

10.3389/fpls.2020.00698

Production and Selection of Quality Protein Popcorn Hybrids Using a Novel Ranking System and Combining Ability Estimates
Cited by: 11
Author(s): Leandra Parsons, Ying Ren, Abou Yobi, Preston Hurst, Ruthie Angelovici, Oscar Rodrı́guez, David R. Holding
Software Mentions: 7
Published: over 4 years ago

10.1038/s41597-020-0544-1

Long-term monitoring of the Iberian ibex population in the Sierra Nevada of the southeast Iberian Peninsula
Cited by: 7
Author(s): José E. Granados, Andrea Ros-Candeira, Antonio J. Pérez‐Luque, Ricardo Moreno-Llorca, Francisco Javier Cano-Manuel, Paulino Fandós, Ramón C. Soriguer, José Espinosa Cerrato, Jesús M. Pérez, Blanca Cecilia Ramos, Regino Zamora
Software Mentions: 7
Published: over 4 years ago

10.1186/s12859-019-2899-x

Efficient estimation of grouped survival models
Cited by: 0
Author(s): Zhiguo Li, Jiaxing Lin, Alexander B. Sibley, Tracy Truong, Katherina C. Chua, Yu Jiang, Janice McCarthy, Deanna L. Kroetz, Andrew S. Allen, Kouros Owzar
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2021.695415

Leaf Epidermis: The Ambiguous Symplastic Domain
Cited by: 0
Author(s): Olga V. Voitsekhovskaja, Anna N. Melnikova, Kirill N. Demchenko, Alexandra N. Ivanova, V. A. Dmitrieva, Anastasiia I. Maksimova, Gertrud Lohaus, A. D. Tomos, E.V. Tyutereva, Olga Koroleva
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0232682

A chronological model for the Late Paleolithic at Shuidonggou Locality 2, North China
Cited by: 10
Author(s): Fei Peng, Sam C. Lin, Ilaria Patania, Vladimir Levchenko, Jialong Guo, Huimin Wang, Xing Gao
Software Mentions: 7
Published: over 4 years ago

10.12688/f1000research.11840.4

GAC: Gene Associations with Clinical, a web based application
Cited by: 1
Author(s): Xinyan Zhang, Manali Rupji, Jeanne Kowalski
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12864-019-5924-6

A catalog of CasX genome editing sites in common model organisms
Cited by: 4
Author(s): Elisha D.O. Roberson
Software Mentions: 7
Published: over 5 years ago

10.1007/s00277-020-04362-2

Letermovir prophylaxis is effective in preventing cytomegalovirus reactivation after allogeneic hematopoietic cell transplantation: single-center real-world data
Cited by: 21
Author(s): Patrick Derigs, Aleksandar Radujkovic, Maria‐Luisa Schubert, Paul Schnitzler, Tilman Schöning, Carsten Müller‐Tidow, Ute Hegenbart, Stefan Schönland, Thomas Luft, Peter Dreger, Michael Schmitt
Software Mentions: 7
Published: almost 4 years ago

10.1186/1471-2105-15-138

An R package that automatically collects and archives details for reproducible computing
Cited by: 15
Author(s): Zhifa Liu, Stanley Pounds
Software Mentions: 6
Published: over 10 years ago

10.12688/f1000research.10232.1

Approaches to R education in Canadian universities
Cited by: 2
Author(s): M. A. Carson, Nathan Basiliko
Software Mentions: 6
Published: almost 8 years ago

10.1038/s41598-021-90409-x

High-throughput phenotyping methods for quantifying hair fiber morphology
Cited by: 1
Author(s): Tina Lasisi, Arslan Zaidi, Timothy H. Webster, Nicholas Stephens, Kendall Routch, Nina G. Jablonski, Mark D. Shriver
Software Mentions: 6
Published: over 3 years ago

10.1080/17453674.2019.1624339

Reduced periprosthetic fracture rate when changing from a tapered polished stem to an anatomical stem for cemented hip arthroplasty: an observational prospective cohort study with a follow-up of 2 years
Cited by: 17
Author(s): Jabbar Mohammed, Sebastian Mukka, Carl-Johan Hedbeck, Ghazi Chammout, Max Gordon, Olof Sköldenberg
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2019.01569

The Impact of Surgery in IDH 1 Wild Type Glioblastoma in Relation With the MGMT Deregulation
Cited by: 13
Author(s): Francesco Marchi, Nora Sahnane, Roberta Cerutti, Debora Cipriani, Jessica Barizzi, Federico Mattia Stefanini, Samantha Epistolio, Michele Cerati, Sergio Balbi, Luca Mazzucchelli, Fausto Sessa, G. Pesce, Michael Reinert, Milo Frattini
Software Mentions: 6
Published: almost 5 years ago

10.3390/toxins11010019

Interannual Variability of Dinophysis acuminata and Protoceratium reticulatum in a Chilean Fjord: Insights from the Realized Niche Analysis
Cited by: 23
Author(s): Catharina Alves‐de‐Souza, José Luis Iriarte, Jorge I. Mardones
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-019-42713-w

The effect of numerical aperture on quantitative use-wear studies and its implication on reproducibility
Cited by: 22
Author(s): Ivan Calandra, Lisa Schunk, Konstantin Bob, Walter Gneisinger, Antonella Pedergnana, Eduardo Paixão, Andreas Hildebrandt, João Marreiros
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0071090

Glocal Clinical Registries: Pacemaker Registry Design and Implementation for Global and Local Integration – Methodology and Case Study
Cited by: 29
Author(s): Kátia Regina da Silva, Roberto Costa, Elizabeth Sartori Crevelari, Marianna Sobral Lacerda, Caio Marcos de Moraes Albertini, Martino Martinelli Filho, José Eduardo Santana, João Ricardo Nickenig Vissoci, Ricardo Pietrobon, Jacson Venâncio de Barros
Software Mentions: 6
Published: over 11 years ago

10.3389/fpsyt.2021.697127

Daily-Life Social Experiences as a Potential Mediator of the Relationship Between Parenting and Psychopathology in Adolescence
Cited by: 6
Author(s): Robin Achterhof, Olivia J. Kirtley, Maude Schneider, Ginette Lafit, Noëmi Hagemann, Karlijn Susanna Francisca Maria Hermans, Anu P. Hiekkaranta, Aleksandra Lecei, Inez Myin-Germeys
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2020.565626

A Near-Chromosome Level Genome Assembly of Anopheles stephensi
Cited by: 14
Author(s): Afiya Razia Chida, Samathmika Ravi, Suvratha Jayaprasad, Kiran Paul, Jaysmita Saha, Chinjusha Suresh, Saurabh Whadgar, Naveen Kumar, Raksha Rao K, Chaitali Ghosh, Bibha Choudhary, Suresh Subramani, Subhashini Srinivasan
Software Mentions: 6
Published: about 4 years ago

10.1093/emph/eow013

The low prevalence of female smoking in the developing world: gender inequality or maternal adaptations for fetal protection?
Cited by: 28
Author(s): Edward H. Hagen, Melissa J. Garfield, Roger J. Sullivan
Software Mentions: 6
Published: almost 9 years ago

10.12688/f1000research.13049.2

RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting
Cited by: 6
Author(s): Travis L. Jensen, Michael Frasketi, Kevin P. Conway, Leigh Villarroel, Heather Hill, Konstantinos Krampis, Johannes Goll
Software Mentions: 6
Published: over 6 years ago

Projects: cran: knitr

Papers Mentioning knitr 157