Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: plotly
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/plotly
Create Interactive Web Graphics via 'plotly.js'
24 versions
Latest release: about 1 year ago
418 dependent packages
295,938 downloads last month
Papers Mentioning plotly 163
10.1371/journal.pcbi.1007912
bigPint: A Bioconductor visualization package that makes big data pint-sizedCited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago
10.1038/s41598-019-54004-5
An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolatesCited by: 61
Author(s): Arun Gonzales Decano, Tim Downing
Software Mentions: 30
Published: almost 5 years ago
10.1186/s12859-017-1905-4
ADAGE signature analysis: differential expression analysis with data-defined gene setsCited by: 15
Author(s): Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Software Mentions: 25
Published: almost 7 years ago
10.7717/peerj.6398
Quantitative color profiling of digital images with earth mover’s distance using the R package colordistanceCited by: 49
Author(s): Hannah Weller, Mark W. Westneat
Software Mentions: 23
Published: over 5 years ago
10.3389/fvets.2020.547181
Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in QuébecCited by: 9
Author(s): Catherine Turcotte, Alexandre Thibodeau, Sylvain Quessy, Edward Topp, Guy Beauchamp, Philippe Fravalo, Marie Archambault, Marie-Lou Gaucher
Software Mentions: 23
Published: almost 4 years ago
10.1016/j.xcrm.2020.100128
The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of CancerCited by: 32
Author(s): Derek J. Essegian, Rimpi Khurana, Vasileios Stathias, Stephan C. Schürer
Software Mentions: 21
Published: about 4 years ago
10.3389/fimmu.2021.632333
Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic MiceCited by: 7
Author(s): Panpan Yang, Lu Liu, Lili Sun, Fang Pu, Nathaniel W. Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang
Software Mentions: 21
Published: over 3 years ago
10.1016/j.csbj.2019.10.003
MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize linesCited by: 9
Author(s): Wei Zhou, Lei Wang, Wenming Zheng, Wen Yao
Software Mentions: 20
Published: almost 6 years ago
10.1186/s13104-019-4179-2
TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count dataCited by: 75
Author(s): Wei Su, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 20
Published: over 5 years ago
10.1371/journal.pone.0247002
Chainchecker: An application to visualise and explore transmission chains for Ebola virus diseaseCited by: 2
Author(s): Katy A. M. Gaythorpe, Aaron Morris, Natsuko Imai, Miles Stewart, Jeffrey S. Freeman, Mary J. Choi
Software Mentions: 19
Published: over 3 years ago
10.1038/s41598-020-73413-5
The macroevolutionary landscape of short-necked plesiosauriansCited by: 13
Author(s): Valentin Fischer, Jamie A. MacLaren, Laura C. Soul, Rebecca Bennion, Patrick S. Druckenmiller, Roger Benson
Software Mentions: 19
Published: about 4 years ago
10.1093/bioinformatics/bty947
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics dataCited by: 19
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 18
Published: almost 6 years ago
10.1186/s40168-019-0702-x
Understanding microbial community dynamics to improve optimal microbiome selectionCited by: 193
Author(s): Robyn J. Wright, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 18
Published: over 5 years ago
10.3389/fgene.2019.00499
ABioTrans: A Biostatistical Tool for Transcriptomics AnalysisCited by: 6
Author(s): Zou Yutong, Thuy Tien Bui, Kumar Selvarajoo
Software Mentions: 17
Published: over 5 years ago
10.1371/journal.pone.0232822
SimSurvey: An R package for comparing the design and analysis of surveys by simulating spatially-correlated populationsCited by: 5
Author(s): Paul M. Regular, Gregory J. Robertson, Keith P. Lewis, Jonathan Babyn, Brian Healey, Fran Mowbray
Software Mentions: 17
Published: over 4 years ago
10.3389/fvets.2021.620327
Detection of Mycobacterium avium ssp. paratuberculosis in Cultures From Fecal and Tissue Samples Using VOC Analysis and Machine Learning ToolsCited by: 6
Author(s): Philipp Vitense, Elisa Kasbohm, Anne Klassen, Peter Gierschner, Phillip Trefz, M. Weber, Wolfram Miekisch, Jochen K. Schubert, Petra Möbius, Petra Reinhold, Volkmar Liebscher, Heike Köhler
Software Mentions: 17
Published: almost 4 years ago
10.1073/pnas.2006024117
Diel variability of methane emissions from lakesCited by: 46
Author(s): Anna Sieczko, Nguyen Thanh Duc, Jonathan Schenk, Gustav Pajala, David Rudberg, Henrique O. Sawakuchi, David Bastviken
Software Mentions: 17
Published: about 4 years ago
10.3390/cells10082013
ChroMo, an Application for Unsupervised Analysis of Chromosome Movements in MeiosisCited by: 0
Author(s): Daniel León-Periñán, Alfonso Fernández-Álvarez
Software Mentions: 17
Published: over 3 years ago
10.1371/journal.pcbi.1006245
Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools databaseCited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago
10.1038/s41598-021-81583-z
Foraging niche partitioning in sympatric seabird populationsCited by: 11
Author(s): Christina Petalas, Thomas Lazarus, Richard Lavoie, Kyle H. Elliott, Mélanie F. Guigueno
Software Mentions: 16
Published: almost 4 years ago
10.1371/journal.pntd.0009232
Intestinal protozoan infections shape fecal bacterial microbiota in children from Guinea-BissauCited by: 8
Author(s): Sebastian von Huth, Louise B. Thingholm, Poul Erik Kofoed, Corinna Bang, Malte Rühlemann, André Franke, Uffe Holmskov
Software Mentions: 15
Published: over 3 years ago
10.1038/s41598-021-81200-z
MuSA: a graphical user interface for multi-OMICs data integration in radiogenomic studiesCited by: 11
Author(s): Mario Zanfardino, Rossana Castaldo, Katia Pane, Ornella Affinito, Marco Aiello, Marco Salvatore, Monica Franzese
Software Mentions: 15
Published: almost 4 years ago
10.1093/jas/skaa402
ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1Cited by: 4
Author(s): Gota Morota, Hao Cheng, Dianne Cook, Emi Tanaka
Software Mentions: 15
Published: almost 4 years ago
10.1371/journal.pone.0240935
The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genomeCited by: 24
Author(s): Kris A. Christensen, Eric B. Rondeau, David R. Minkley, Dionne Sakhrani, Carlo A. Biagi, Anne-Marie Flores, Ruth E. Withler, Scott A. Pavey, Terry D. Beacham, Theresa Godin, Eric B. Taylor, Michael A. Russello, Robert H. Devlin, Ben F. Koop
Software Mentions: 15
Published: about 4 years ago
10.3389/fchem.2021.734132
The “DOLPHINS” Project: A Low-Cost Real-Time Multivariate Process Control From Large Sensor Arrays Providing Sparse Binary DataCited by: 1
Author(s): Eugenio Alladio, Marcello Baricco, Vincenzo Leogrande, Renato Pagliari, Fabio Pozzi, Paolo Foglio, Marco Vincenti
Software Mentions: 15
Published: about 3 years ago
10.1099/mgen.0.000583
rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence dataCited by: 5
Author(s): Ivan Sserwadda, Gerald Mboowa
Software Mentions: 13
Published: over 3 years ago
10.2196/16810
Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort StudyCited by: 29
Author(s): Benjamin S. Glicksberg, Shohei Burns, R. Currie, A. Clark Griffin, Zhen Jane Wang, David Haussler, Theodore C. Goldstein, Eric A. Collisson
Software Mentions: 13
Published: over 4 years ago
10.1186/s13073-021-00904-z
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibilityCited by: 33
Author(s): Liuyang Wang, Thomas J Balmat, Alejandro L. Antonia, Florica J. Constantine, Ricardo Henao, Thomas W. Burke, Andy Ingham, Micah T. McClain, Ephraim L. Tsalik, Emily R Ko, Geoffrey S. Ginsburg, Mark DeLong, Xiling Shen, Christopher W. Woods, Elizabeth R. Hauser, Dennis C. Ko
Software Mentions: 13
Published: over 3 years ago
10.7554/eLife.57116
shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map dataCited by: 35
Author(s): Kenichi Shimada, John A. Bachman, Jeremy Muhlich, Timothy J. Mitchison
Software Mentions: 13
Published: over 3 years ago
10.3389/fpls.2021.628439
The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace AccessionsCited by: 19
Author(s): Marta Liber, Isabel Margarida Duarte, Ana-Teresa Maia, Hugo R. Oliveira
Software Mentions: 13
Published: over 3 years ago
10.3389/fimmu.2021.730346
Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit ImmunogensCited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: about 3 years ago
10.1371/journal.pone.0238835
Analyzing the fine structure of distributionsCited by: 35
Author(s): Michael C. Thrun, Tino Gehlert, Alfred Ultsch
Software Mentions: 12
Published: about 4 years ago
10.3389/fgene.2019.01079
HiCeekR: A Novel Shiny App for Hi-C Data AnalysisCited by: 13
Author(s): Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Maria R. Matarazzo, Claudia Angelini
Software Mentions: 12
Published: about 5 years ago
10.1186/s13567-021-00981-3
Immunogenicity and protective efficacy of a Streptococcus suis vaccine composed of six conserved immunogensCited by: 8
Author(s): Christine Weiße, Denise Dittmar, Beata Jakóbczak, Volker Florian, Nicole Schütze, Gottfried Alber, Kristin Klose, Stephan Michalik, Peter Valentin‐Weigand, Uwe Völker, Christoph Georg Baums
Software Mentions: 12
Published: about 3 years ago
10.1002/cam4.3907
MRPL15 is a novel prognostic biomarker and therapeutic target for epithelial ovarian cancerCited by: 21
Author(s): Haoya Xu, Ruoyao Zou, Feifei Li, Jiyu Liu, Nannan Luan, Shengke Wang, Liping Zhu
Software Mentions: 12
Published: over 3 years ago
10.1371/journal.pone.0229330
StructuRly: A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysisCited by: 22
Author(s): Nicola G. Criscuolo, Claudia Angelini
Software Mentions: 12
Published: over 4 years ago
10.1186/s12859-018-2105-6
Building protein-protein interaction networks for Leishmania species through protein structural informationCited by: 17
Author(s): Crhisllane Rafaele dos Santos Vasconcelos, Túlio de Lima Campos, Antônio Mauro Rezende
Software Mentions: 11
Published: over 6 years ago
10.1038/s41598-018-31154-6
Instant Clue: A Software Suite for Interactive Data Visualization and AnalysisCited by: 156
Author(s): Hendrik Nolte, Thomas MacVicar, Frederik Tellkamp, Marcus Krüger
Software Mentions: 11
Published: about 6 years ago
10.3389/fimmu.2016.00339
IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUESTCited by: 38
Author(s): Safa Aouinti, Véronique Giudicelli, Patrice Duroux, Dhafer Malouche, Sofia Kossida, Marie‐Paule Lefranc
Software Mentions: 11
Published: about 8 years ago
10.1186/s41044-019-0043-6
A substrate for modular, extensible data-visualizationCited by: 6
Author(s): Jordan Matelsky, Joseph Downs, Hannah Cowley, Brock Wester, William Gray-Roncal
Software Mentions: 11
Published: over 4 years ago
10.3389/fninf.2019.00012
A Serverless Tool for Platform Agnostic Computational Experiment ManagementCited by: 13
Author(s): Gregory Kiar, Shawn T. Brown, Tristan Glatard, Alan C. Evans
Software Mentions: 11
Published: over 5 years ago
10.1038/s41598-020-65015-y
Toffee – a highly efficient, lossless file format for DIA-MSCited by: 9
Author(s): Brett Tully
Software Mentions: 11
Published: over 4 years ago
10.1186/s13104-017-2607-8
NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networksCited by: 28
Author(s): Θεοδόσιος Θεοδοσίου, Georgios Efstathiou, Nikolas Papanikolaou, Nikos C. Kyrpides, Pantelis G. Bagos, Ioannis Iliopoulos, Georgios A. Pavlopoulos
Software Mentions: 11
Published: over 7 years ago
10.1111/1755-0998.13220
High‐contiguity genome assembly of the chemosynthetic gammaproteobacterial endosymbiont of the cold seep tubeworm <i>Lamellibrachia barhami</i>Cited by: 6
Author(s): Corinna Breusing, Darrin T. Schultz, Sebastian Sudek, Alexandra Z. Worden, Charles W. Young
Software Mentions: 11
Published: over 4 years ago
10.1038/s41598-021-94324-z
Modest changes in Spi1 dosage reveal the potential for altered microglial function as seen in Alzheimer’s diseaseCited by: 17
Author(s): Ruth Jones, Robert Andrews, Peter Holmans, Matthew Hill, Philip R. Taylor
Software Mentions: 11
Published: over 3 years ago
10.1186/s12859-019-2968-1
Visualization methods for differential expression analysisCited by: 6
Author(s): Lindsay Rutter, Adrienne N. Moran Lauter, Michelle A. Graham, Dianne Cook
Software Mentions: 11
Published: about 5 years ago
10.1371/journal.pone.0238496
Lyme disease and relapsing fever in Mexico: An overview of human and wildlife infectionsCited by: 18
Author(s): Pablo Colunga‐Salas, Sokani Sánchez‐Montes, Patricia Volkow, Adriana Ruíz-Remigio, Ingeborg Becker
Software Mentions: 10
Published: about 4 years ago
10.1093/bib/bbv108
Dimension reduction techniques for the integrative analysis of multi-omics dataCited by: 262
Author(s): Chen Meng, Oana A. Zeleznik, Gerhard G. Thallinger, Bernhard Küster, Amin Moghaddas Gholami, Aedín C. Culhane
Software Mentions: 10
Published: over 8 years ago
10.1099/mgen.0.000552
Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogenCited by: 6
Author(s): Josephine Grützke, Mayada Gwida, Carlus Deneke, Holger Brendebach, Michaela Projahn, Alexander Schattschneider, Dirk Hofreuter, Maged El-Ashker, Burkhard Malorny, Sascha Al Dahouk
Software Mentions: 10
Published: over 3 years ago
10.3389/fmed.2020.00247
Growth Rate and Acceleration Analysis of the COVID-19 Pandemic Reveals the Effect of Public Health Measures in Real TimeCited by: 34
Author(s): Yuri Tani Utsunomiya, Adam Taiti Harth Utsunomiya, Rafaela Beatriz Pintor Torrecilha, Silvana de Cássia Paulan, Marco Milanesi, José Fernando Garcia
Software Mentions: 10
Published: over 4 years ago
10.1016/j.dib.2020.105195
Dataset of depressive posts in Russian language collected from social mediaCited by: 12
Author(s): Sergazy Narynov, Daniyar Mukhtarkhanuly, Batyrkhan Omarov
Software Mentions: 10
Published: over 4 years ago
10.1186/s40168-019-0745-z
Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantationCited by: 57
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Malene Skovsted Cilieborg, Ole Lund, Susan Holmes, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 9
Published: about 5 years ago
10.12688/f1000research.27062.2
SAPHIR: a Shiny application to analyze tissue section imagesCited by: 0
Author(s): Elodie Germani, Hugues Lelouard, Mathieu Fallet
Software Mentions: 9
Published: over 3 years ago
10.3389/fcell.2020.00268
Comparative Transcriptome Landscape of Mouse and Human HeartsCited by: 14
Author(s): Tatsuya Anzai, Takanori Yamagata, Hideki Uosaki
Software Mentions: 9
Published: over 4 years ago
10.3389/fmicb.2021.654135
Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, AntarcticaCited by: 3
Author(s): Adam J. Solon, Claire F. Mastrangelo, Lara Vimercati, Pacifica Sommers, John L. Darcy, Eli M. S. Gendron, Dorota L. Porazinska, Steven K. Schmidt
Software Mentions: 9
Published: over 3 years ago
10.1093/bioinformatics/btaa838
<i>MicrobiomeExplorer</i>: an R package for the analysis and visualization of microbial communitiesCited by: 16
Author(s): Janina Reeder, Mo Huang, Joshua S. Kaminker, Joseph N. Paulson
Software Mentions: 9
Published: about 4 years ago
10.3390/cancers13061189
Pan-Cancer Analysis of Human Kinome Gene Expression and Promoter DNA Methylation Identifies Dark Kinase Biomarkers in Multiple CancersCited by: 10
Author(s): Siddesh Southekal, Nitish K. Mishra, Chittibabu Guda
Software Mentions: 9
Published: over 3 years ago
10.3389/fmolb.2021.683671
Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctataCited by: 7
Author(s): Florian Schindler, Lena Fragner, Johannes B Herpell, Andreas Berger, Martin Brenner, Sonja Tischler, Anke Bellaire, Jürg Schönenberger, Weimin Liu, Xiaoliang Sun, Johann Schinnerl, Lothar Brecker, Wolfram Weckwerth
Software Mentions: 9
Published: over 3 years ago
10.1186/s12859-020-03669-1
TRIP - T cell receptor/immunoglobulin profilerCited by: 11
Author(s): Maria Th. Kotouza, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou, Fotis Psomopoulos
Software Mentions: 9
Published: about 4 years ago
10.1186/s12864-018-4870-z
WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing dataCited by: 11
Author(s): Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser, Kelly V. Ruggles
Software Mentions: 9
Published: over 6 years ago
10.1371/journal.pone.0199841
Spatially explicit action research for coastal fisheries managementCited by: 7
Author(s): Tara N. Lawrence, R. S. Bhalla
Software Mentions: 8
Published: over 6 years ago
10.3390/ijms22179211
Extracellular Vesicle Separation Techniques Impact Results from Human Blood Samples: Considerations for Diagnostic ApplicationsCited by: 12
Author(s): Theophilos Tzaridis, Daniel Bachurski, Shu Liu, Kristin Surmann, Felix Babatz, Manuela Gesell Salazar, Uwe Völker, Michael Hallek, Ulrich Herrlinger, Ina Vorberg, Christoph Coch, Katrin S. Reiners, Gunther Hartmann
Software Mentions: 8
Published: about 3 years ago
10.1093/bioinformatics/btaa093
Methplotlib: analysis of modified nucleotides from nanopore sequencingCited by: 22
Author(s): Wouter De Coster, Endre Bakken Stovner, Mojca Stražišar
Software Mentions: 8
Published: over 4 years ago
10.1093/aobpla/plaa019
Genetic variation in early fitness traits across European populations of silver birch (Betula pendula)Cited by: 7
Author(s): Aida Solé-Medina, Katrin Heer, Lars Opgenoorth, Phillip Kaldewey, Darius Danusevičius, Eduardo Notivol, Juan J. Robledo‐Arnuncio, José Alberto Ramírez‐Valiente
Software Mentions: 8
Published: over 4 years ago
10.1186/s12859-021-04166-9
PTMViz: a tool for analyzing and visualizing histone post translational modification dataCited by: 4
Author(s): Kevin Chappell, Stefan Graw, Charity L. Washam, Aaron J. Storey, Chris Bolden, Eric C. Peterson, Stephanie D. Byrum
Software Mentions: 8
Published: over 3 years ago
10.12688/f1000research.13541.1
archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systemsCited by: 20
Author(s): Benjamin Delory, Li Mao, Christopher N. Topp, Guillaume Lobet
Software Mentions: 8
Published: almost 7 years ago
10.3389/fvets.2020.00523
Mind the Queue: A Case Study in Visualizing Heterogeneous Behavioral Patterns in Livestock Sensor Data Using Unsupervised Machine Learning TechniquesCited by: 11
Author(s): Catherine McVey, Fushing Hsieh, Diego Manríquez, Pablo Pinedo, Kristina Horback
Software Mentions: 8
Published: about 4 years ago
10.3389/fpsyg.2019.02597
Native Language Influence on Brass Instrument Performance: An Application of Generalized Additive Mixed Models (GAMMs) to Midsagittal Ultrasound Images of the TongueCited by: 9
Author(s): Matthias Heyne, Donald Derrick, Jalal Al-Tamimi
Software Mentions: 8
Published: almost 5 years ago
10.7554/eLife.64513
Chondrocytes in the resting zone of the growth plate are maintained in a Wnt-inhibitory environmentCited by: 25
Author(s): Shawn A Hallett, Yuki Matsushita, Wanida Ono, Naoko Sakagami, Koji Mizuhashi, Nicha Tokavanich, Mizuki Nagata, Annabelle Zhou, Takao Hanabusa, Henry M. Kronenberg, Noriaki Ono
Software Mentions: 8
Published: over 3 years ago
10.1186/s12864-021-07898-3
Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair eventsCited by: 4
Author(s): Ümit Akköse, Veysel Oğulcan Kaya, Laura A. Lindsey-Boltz, Zeynep Karagöz, Adam D. Brown, Peter A. Larsen, Anne D. Yoder, Aziz Sancar, Ogün Adebali
Software Mentions: 8
Published: over 3 years ago
10.3390/s21092964
Traffic Congestion Analysis Based on a Web-GIS and Data Mining of Traffic Events from TwitterCited by: 17
Author(s): Juan Salazar-Carrillo, Miguel Torres-Ruiz, Clodoveu A. Davis, Rolando Quintero, Marco Moreno-Ibarra, Giovanni Guzmán
Software Mentions: 8
Published: over 3 years ago
10.3390/plants10081594
RNAi Suppression of LEAFY Gives Stable Floral Sterility, and Reduced Growth Rate and Leaf Size, in Field-Grown PoplarsCited by: 5
Author(s): Amy L. Klocko, Amanda Goddard, Jeremy R. Jacobson, Anna Magnuson, S. H. Strauss
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pbio.3000988
The molecular and metabolic program by which white adipocytes adapt to cool physiologic temperaturesCited by: 9
Author(s): Hiroyuki Mori, Colleen E. Dugan, Akira Nishii, Ameena Benchamana, Ziru Li, Thomas S. Cadenhead, Arun K. Das, Charles R. Evans, Katherine A. Overmyer, Steven M. Romanelli, Sydney K. Peterson, Devika P. Bagchi, Callie A.S. Corsa, Julie Hardij, Brian S. Learman, Mahmoud El Azzouny, Joshua J. Coon, Ken Inoki, Ormond A. MacDougald
Software Mentions: 7
Published: over 3 years ago
10.1038/s41598-019-43875-3
Gut microbiome differences between wild and captive black rhinoceros – implications for rhino healthCited by: 77
Author(s): Keylie M. Gibson, Bryan Nguyen, Laura Neumann, Michele A. Miller, Peter Buss, Savel R. Daniels, Michelle Ahn, Keith A. Crandall, Budhan S. Pukazhenthi
Software Mentions: 7
Published: over 5 years ago
10.1186/s12859-018-2435-4
Single sample scoring of molecular phenotypesCited by: 230
Author(s): Momeneh Foroutan, Dharmesh D. Bhuva, Ruqian Lyu, Kristy Horan, Joseph Cursons, Melissa J. Davis
Software Mentions: 7
Published: almost 6 years ago
10.1186/s12859-021-04392-1
shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case studyCited by: 1
Author(s): Sonia Olaechea-Lázaro, Iraia García-Santisteban, José Ramón Pineda, Iker Badiola, Santos Alonso, José Ramón Bilbao, Nora Fernández-Jiménez
Software Mentions: 7
Published: about 3 years ago
10.1038/s41598-019-52294-3
Oct4-mediated reprogramming induces embryonic-like microRNA expression signatures in human fibroblastsCited by: 16
Author(s): Lucie Pešková, Kateřina Černá, Jan Oppelt, Marek Mráz, Tomáš Bárta
Software Mentions: 7
Published: about 5 years ago
10.1371/journal.pone.0176334
shinyheatmap: Ultra fast low memory heatmap web interface for big data genomicsCited by: 97
Author(s): Bohdan B. Khomtchouk, John L. Hennessy, Claes Wahlestedt
Software Mentions: 7
Published: over 7 years ago
10.1074/jbc.RA119.008853
Transcriptional profiling of single fiber cells in a transgenic paradigm of an inherited childhood cataract reveals absence of molecular heterogeneityCited by: 4
Author(s): Suraj P. Bhat, Rajendra K. Gangalum, Dongjae Kim, Serghei Mangul, Raj K. Kashyap, Xinkai Zhou, David Elashoff
Software Mentions: 7
Published: about 5 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 chromosomesCited by: 2
Author(s): Yasmine Mansour, Annie Château, Anna-Sophie Fiston-Lavier
Software Mentions: 7
Published: over 3 years ago
10.3390/molecules25153402
The Mineral Profile of Polish Beers by Fast Sequential Multielement HR CS FAAS Analysis and Its Correlation with Total Phenolic Content and Antioxidant Activity by Chemometric MethodsCited by: 8
Author(s): Elżbieta Zambrzycka-Szelewa, Edyta Nalewajko-Sieliwoniuk, Mariusz Zaremba, Andrzej Bajguz, Beata Godlewska‐Żyłkiewicz
Software Mentions: 7
Published: over 4 years ago
10.1186/s12885-017-3689-3
GRcalculator: an online tool for calculating and mining dose–response dataCited by: 57
Author(s): Nicholas Clark, Marc Hafner, Michal Kouril, Liz Williams, Jeremy Muhlich, Marcin Pilarczyk, Mario Niepel, Peter K. Sorger, Mario Medvedovic
Software Mentions: 7
Published: about 7 years ago
10.3389/fmicb.2021.664542
Nutrient-Poor Breeding Substrates of Ambrosia Beetles Are Enriched With Biologically Important ElementsCited by: 10
Author(s): Maximilian Lehenberger, Nina Foh, Axel Göttlein, Diana L. Six, Peter H. W. Biedermann
Software Mentions: 7
Published: over 3 years ago
10.3390/cells9020458
Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice SitesCited by: 25
Author(s): Karl Frey, Boas Pucker
Software Mentions: 7
Published: over 4 years ago
10.3389/fgene.2019.00971
Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP WebtoolCited by: 15
Author(s): André Nicolau Aquime Gonçalves, Melissa Lever, Pedro Russo, Bruno Gomes-Correia, Alysson H. Urbanski, Gabriele Pollara, Mahdad Noursadeghi, Vinicius Maracaja‐Coutinho, Helder I. Nakaya
Software Mentions: 7
Published: about 5 years ago
10.3389/fcell.2021.702046
Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous TrophoblastCited by: 17
Author(s): Robert Morey, Omar Farah, Sampada Kallol, Daniela F. Requena, Morgan Meads, Matteo Moretto-Zita, Francesca Soncin, Louise C. Laurent, Mana M. Parast
Software Mentions: 7
Published: about 3 years ago
10.3390/s21165473
Generator of Slow Denial-of-Service Cyber AttacksCited by: 6
Author(s): Marek Sikora, Radek Fujdiak, Karel Kuchař, Eva Holasová, Jiří Mišurec
Software Mentions: 7
Published: about 3 years ago
10.1371/journal.pcbi.1007654
ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS dataCited by: 28
Author(s): Lisa Bramer, A. M. White, Kelly G. Stratton, Allison Thompson, Daniel Claborne, Kirsten Hofmockel, Lee Ann McCue
Software Mentions: 7
Published: over 4 years ago
10.5334/jors.166
Web Tool for Navigating and Plotting SomaLogic ADAT FilesCited by: 19
Author(s): Foo Cheung, Giovanna Fantoni, Maria Conner, Brian Sellers, Yuri Kotliarov, Julián Candia, Katherine E. Stagliano, Angélique Biancotto
Software Mentions: 6
Published: about 7 years ago
10.1186/s12859-020-3434-9
SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python frameworkCited by: 7
Author(s): Martin Lewinski, Yannik Bramkamp, Tino Köster, Dorothee Staiger
Software Mentions: 6
Published: over 4 years ago
10.1186/s12859-019-3320-5
DynaVenn: web-based computation of the most significant overlap between ordered setsCited by: 14
Author(s): Jérémy Amand, Tobias Fehlmann, Christina Backes, Andreas Keller
Software Mentions: 6
Published: almost 5 years ago
10.1007/s00429-021-02358-w
Dissecting whole-brain conduction delays through MRI microstructural measuresCited by: 6
Author(s): Matteo Mancini, Qiyuan Tian, Qiuyun Fan, Mara Cercignani, Susie Y. Huang
Software Mentions: 6
Published: about 3 years ago
10.1002/1878-0261.12786
Allele‐specific proximal promoter hypomethylation of the telomerase reverse transcriptase gene (<i>TERT</i>) associates with <i>TERT</i> expression in multiple cancersCited by: 20
Author(s): Teisha J. Rowland, Andrew J. Bonham, Thomas R. Cech
Software Mentions: 6
Published: about 4 years ago
10.7717/peerj.10050
Are giant clams (<i>Tridacna maxima</i>) distractible? A multi-modal studyCited by: 6
Author(s): Ryan Doyle, Jonathan Kim, Angelika Pe, Daniel T. Blumstein
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pone.0211608
Managing genomic variant calling workflows with Swift/TCited by: 7
Author(s): Azza E. Ahmed, Jacob R Heldenbrand, Yan W. Asmann, Faisal M. Fadlelmola, Daniel S. Katz, Katherine Kendig, Matthew Kendzior, Tiffany Li, Yingxue Ren, Elliott Rodriguez, Matthew Weber, Justin M. Wozniak, Jennie Zermeno, Liudmila Sergeevna Mainzer
Software Mentions: 6
Published: over 5 years ago
10.3389/fgene.2020.00730
ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic VariantsCited by: 3
Author(s): Mohith Manjunath, Yi Zhang, Shilu Zhang, Sushmita Roy, Pablo Pérez-Piñera, Jun S. Song
Software Mentions: 6
Published: over 4 years ago
10.1093/gigascience/giab003
long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing dataCited by: 25
Author(s): Shanika L. Amarasinghe, Matthew E. Ritchie, Quentin Gouil
Software Mentions: 6
Published: almost 4 years ago
10.1038/s41597-020-00731-8
CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US countiesCited by: 10
Author(s): Douglas Arneson, Matthew Elliott, Arman Mosenia, Boris Oskotsky, Samuel Solodar, Rohit Vashisht, Travis Zack, Paul A. Bleicher, Atul J. Butte, Vivek Rudrapatna
Software Mentions: 6
Published: almost 4 years ago
10.1128/mSphere.00454-19
Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile InfectionCited by: 24
Author(s): David B. Stewart, Justin Wright, Maria Fowler, Christopher J. McLimans, Vasily Tokarev, Isabella Amaniera, Owen Baker, Hoi‐Tong Wong, Jeffrey L. Brabec, Rebecca Drucker, Regina Lamendella
Software Mentions: 6
Published: about 5 years ago
10.1101/2020.04.28.20083279
CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US countiesCited by: 1
Author(s): Douglas Arneson, Matthew Elliott, Arman Mosenia, Boris Oskotsky, Rohit Vashisht, Travis Zack, Paul A. Bleicher, Atul J. Butte, Vivek Rudrapatna
Software Mentions: 6
Published: over 4 years ago