cran: shiny | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1007912

bigPint: A Bioconductor visualization package that makes big data pint-sized
Cited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago

Protocol for Identification and Removal of Doublets with DoubletDecon
Cited by: 7
Author(s): Erica A. K. DePasquale, Daniel Schnell, Kashish Chetal, Nathan Salomonis
Software Mentions: 25
Published: over 4 years ago

10.1038/s41598-020-74015-x

Rural–urban scaling of age, mortality, crime and property reveals a loss of expected self-similar behaviour
Cited by: 7
Author(s): Jack Sutton, Golnaz Shahtahmassebi, Haroldo V. Ribeiro, Quentin S. Hanley
Software Mentions: 24
Published: about 4 years ago

10.7554/eLife.43966

Unified single-cell analysis of testis gene regulation and pathology in five mouse strains
Cited by: 91
Author(s): Min Jung, Daniel Wells, Jannette Rusch, Suhaira Ahmad, Jonathan Marchini, Simon Myers, Donald F. Conrad
Software Mentions: 22
Published: over 5 years ago

10.3389/fgene.2019.00594

BioNetStat: A Tool for Biological Networks Differential Analysis
Cited by: 21
Author(s): Vinícius Carvalho Jardim, Suzana de Siqueira Santos, André Fujita, Marcos Silveira Buckeridge
Software Mentions: 22
Published: over 5 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 Cancer
Cited by: 32
Author(s): Derek J. Essegian, Rimpi Khurana, Vasileios Stathias, Stephan C. Schürer
Software Mentions: 21
Published: about 4 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: almost 6 years ago

10.1016/j.csbj.2019.10.003

MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines
Cited by: 9
Author(s): Wei Zhou, Lei Wang, Wenming Zheng, Wen Yao
Software Mentions: 20
Published: almost 6 years ago

10.1186/s13059-019-1805-1

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: about 5 years ago

10.7717/peerj.9539

The importance of open science for biological assessment of aquatic environments
Cited by: 15
Author(s): Marcus W. Beck, Casey C. O’Hara, Julia S. Stewart Lowndes, Raphael D. Mazor, Susanna Theroux, David J. Gillett, Belize Lane, Gregory Gearheart
Software Mentions: 17
Published: over 4 years ago

10.1038/s41598-020-71344-9

Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State
Cited by: 9
Author(s): Laura M. Carroll, Jana S. Huisman
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 Tools
Cited 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

10.1371/journal.pone.0135831

CoGA: An R Package to Identify Differentially Co-Expressed Gene Sets by Analyzing the Graph Spectra
Cited by: 18
Author(s): Suzana de Siqueira Santos, Thais Fernanda de Almeida Galatro, Rodrigo Akira Watanabe, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie, André Fujita
Software Mentions: 17
Published: over 9 years ago

10.12688/f1000research.16198.2

scClustViz – Single-cell RNAseq cluster assessment and visualization
Cited by: 25
Author(s): Brendan T. Innes, Gary D. Bader
Software Mentions: 16
Published: almost 6 years ago

10.1186/1471-2105-16-S11-S2

VisRseq: R-based visual framework for analysis of sequencing data
Cited by: 59
Author(s): Hamid Younesy, Torsten B. Möller, Matthew C. Lorincz, Mehdi Karimi, Steven J.M. Jones
Software Mentions: 15
Published: over 9 years ago

10.1186/s12920-017-0261-6

CVE: an R package for interactive variant prioritisation in precision oncology
Cited by: 6
Author(s): Andreas Möck, Suzanne Murphy, James A. Morris, Francesco Marass, Nitzan Rosenfeld, Charles E. Massie
Software Mentions: 14
Published: over 7 years ago

10.1007/s15010-021-01656-z

Prediction of COVID-19 deterioration in high-risk patients at diagnosis: an early warning score for advanced COVID-19 developed by machine learning
Cited by: 16
Author(s): Carolin E. M. Jakob, Ujjwal Mukund Mahajan, Marcus Oswald, Melanie Stecher, Maximilian Schons, Julia Mayerle, Siegbert Rieg, Mathias W. Pletz, Uta Merle, Kai Wille, Stefan Borgmann, Christoph D. Spinner, Sebastian Dolff, Clemens Scherer, Lisa Pilgram, Maria Madeleine Rüthrich, Frank Hanses, Martin Hower, Richard Strauß, Steffen Maßberg, Ahmet Er, Norma Jung, Jörg Janne Vehreschild, Hans Stubbe, Lukas Tometten, Rainer König, Lukas Tometten, Siegbert Rieg, Uta Merle, Kai Wille, Stefan Borgmann, Christoph D. Spinner, Sebastian Dolff, Maria Madeleine Rüthrich, Frank Hanses, Martin Hower, Richard Strauß, Murat Akova, Norma Jung, Michael von Bergwelt‐Baildon, Maria J. G. T. Vehreschild, Beate Grüner, Martina Haselberger, Nora Isberner, Christiane Piepel, Kerstin Hellwig, Dominic Rauschning, Lukas Eberwein, Björn Jensen, Claudia Raichle, Gabriele Müller-Jörger, Sven Stieglitz, Thomas Kratz, Christian Degenhardt, Anette Friedrichs, Robert Bals, Susanne Rüger, Katja de With, Katja Rothfuss, Siri Goepel, Jacob Nattermann, Sabine Jordan, Jessica Rüddel, Janina Trauth, Gernot Beutel, Özlem Altuntaş Aydın, Milena Milovanovic, Michael Doll, Jörg Janne Vehreschild, Lisa Pilgram, Melanie Stecher, Carolin E. M. Jakob, Maximilian Schons, Annika Y. Claßen, Sandra Fuhrmann, Susana Nunes de Miranda, Bernd Franke, Nick Schulze, Fabian Praßer, Martin Lablans
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pbio.3000581

PlotTwist: A web app for plotting and annotating continuous data
Cited by: 43
Author(s): Joachim Goedhart
Software Mentions: 14
Published: almost 5 years ago

10.3390/microorganisms7120680

EpiExploreR: A Shiny Web Application for the Analysis of Animal Disease Data
Cited by: 4
Author(s): Lara Savini, Luca Candeloro, Samuel Perticara, Annamaria Conte
Software Mentions: 14
Published: about 5 years ago

10.1186/s13072-020-00343-x

BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
Cited by: 29
Author(s): Lőrinc Sándor Pongor, Jacob M. Gross, Roberto Vera Alvarez, Junko Murai, Sang‐Min Jang, Hongliang Zhang, Christophe E. Redon, Haiqing Fu, Shar-yin N. Huang, Bhushan Thakur, Adrian Baris, Leonardo Mariño‐Ramírez, David Landsman, Mirit I. Aladjem, Yves Pommier
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 susceptibility
Cited 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

10.1186/s12874-020-01121-9

COVID19-world: a shiny application to perform comprehensive country-specific data visualization for SARS-CoV-2 epidemic
Cited by: 19
Author(s): Cristian Tebé, Joan Valls, Pau Satorra, Aurelio Tobías
Software Mentions: 13
Published: over 4 years ago

10.1128/AEM.01096-17

Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data
Cited by: 58
Author(s): Laura M. Carroll, Jasna Kovač, Robert W. Miller, Martin Wiedmann
Software Mentions: 13
Published: over 7 years ago

10.1186/s12859-019-3251-1

BISR-RNAseq: an efficient and scalable RNAseq analysis workflow with interactive report generation
Cited by: 17
Author(s): Venkat Sundar Gadepalli, Hatice Gülçin Özer, Ayse Selen Yilmaz, Maciej Pietrzak, Amy Webb
Software Mentions: 13
Published: about 5 years ago

10.7554/eLife.57116

shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
Cited by: 35
Author(s): Kenichi Shimada, John A. Bachman, Jeremy Muhlich, Timothy J. Mitchison
Software Mentions: 13
Published: almost 4 years ago

10.1002/ece3.7130

QuoVidi: An open‐source web application for the organization of large‐scale biological treasure hunts
Cited by: 8
Author(s): Guillaume Lobet, Charlotte Descamps, Lola Leveau, Alain Guillet, Jean-François Rees
Software Mentions: 12
Published: almost 4 years ago

10.1371/journal.pone.0229330

StructuRly: A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis
Cited by: 22
Author(s): Nicola G. Criscuolo, Claudia Angelini
Software Mentions: 12
Published: almost 5 years ago

10.1371/journal.pone.0197176

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation
Cited by: 12
Author(s): Selçuk Korkmaz, José M. Duarte, Andreas Prlić, Dinçer Göksülük, Gökmen Zararsız, Osman Saraçbaşı, S.K. Burley, Peter W. Rose
Software Mentions: 12
Published: over 6 years ago

10.1186/s12859-016-1260-x

MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
Cited by: 14
Author(s): Bohdan B. Khomtchouk, John L. Hennessy, Claes Wahlestedt
Software Mentions: 12
Published: over 8 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-QUEST
Cited by: 38
Author(s): Safa Aouinti, Véronique Giudicelli, Patrice Duroux, Dhafer Malouche, Sofia Kossida, Marie‐Paule Lefranc
Software Mentions: 11
Published: over 8 years ago

10.1186/s40064-015-0795-z

Rapid publication-ready MS-Word tables for two-way ANOVA
Cited by: 56
Author(s): Houssein Assaad, Yongqing Hou, Lan Zhou, Raymond J. Carroll, Guoyao Wu
Software Mentions: 11
Published: almost 10 years ago

10.1186/s12859-020-3360-x

ShinyOmics: collaborative exploration of omics-data
Cited by: 11
Author(s): Defne Surujon, Tim van Opijnen
Software Mentions: 11
Published: almost 5 years ago

10.1016/j.epidem.2014.04.003

OutbreakTools: A new platform for disease outbreak analysis using the R software
Cited by: 37
Author(s): Thibaut Jombart, David M. Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Caitlin Collins, Anne Cori, Xavier Didelot, Christophe Fraser, Simon D. W. Frost, Niel Hens, Joseph Hugues, Michael Höhle, Lulla Opatowski, Andrew Rambaut, Oliver Ratmann, Samuel Soubeyrand, Marc A. Suchard, Jacco Wallinga, Rolf J. F. Ypma, Neil M. Ferguson
Software Mentions: 11
Published: over 10 years ago

10.1186/s12859-019-2968-1

Visualization methods for differential expression analysis
Cited by: 6
Author(s): Lindsay Rutter, Adrienne N. Moran Lauter, Michelle A. Graham, Dianne Cook
Software Mentions: 11
Published: over 5 years ago

10.12688/wellcomeopenres.15477.2

Feasibility of informing syndrome-level empiric antibiotic recommendations using publicly available antibiotic resistance datasets
Cited by: 5
Author(s): Quentin J. Leclerc, Nichola R. Naylor, Alexander M. Aiken, Francesc Español i Coll, Gwenan M. Knight
Software Mentions: 11
Published: over 4 years ago

10.1002/ece3.5412

<i>learnPopGen</i> : An R package for population genetic simulation and numerical analysis
Cited by: 6
Author(s): Liam J. Revell
Software Mentions: 10
Published: over 5 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 Time
Cited 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

10.3389/fonc.2021.615321

Development and Validation of a Prognostic Nomogram for Colorectal Cancer Patients With Synchronous Peritoneal Metastasis
Cited by: 8
Author(s): Zifeng Yang, Li Yong, Xiusen Qin, Zejian Lv, Huaiming Wang, Deqing Wu, Zixu Yuan
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.10264

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
Cited by: 6
Author(s): Elly Poretsky, Alisa Huffaker
Software Mentions: 10
Published: about 4 years ago

10.1186/s13046-019-1212-1

The kinase inhibitor SI113 induces autophagy and synergizes with quinacrine in hindering the growth of human glioblastoma multiforme cells
Cited by: 23
Author(s): Silvia Matteoni, Claudia Abbruzzese, Paola Matarrese, Gabriele De Luca, Anna Maria Mileo, Stefania Miccadei, Silvia Schenone, Francesca Musumeci, Tobias Haas, Giovanni Sette, Carmine Maria Carapella, Rosario Amato, Nicola Perrotti, Michele Signore, Marco G. Paggi
Software Mentions: 10
Published: over 5 years ago

10.18632/aging.202748

Development and validation of routine clinical laboratory data derived marker-based nomograms for the prediction of 5-year graft survival in kidney transplant recipients
Cited by: 0
Author(s): Yamei Li, Yan Lin, Yang Li, Zhengli Wan, Yang Bai, Xianding Wang, Shumeng Hu, Xiaojuan Wu, Cuili Yang, Jiwen Fan, Hong‐Xi Xu, Lanlan Wang, Ying Shi
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12859-018-2254-7

Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links
Cited by: 12
Author(s): Abhik Seal, David Wild
Software Mentions: 9
Published: over 6 years ago

10.1186/s12916-020-01826-0

Development and validation of a lifestyle-based model for colorectal cancer risk prediction: the LiFeCRC score
Cited by: 33
Author(s): Krasimira Aleksandrova, Robin Reichmann, Rudolf Kaaks, Mazda Jenab, H. Bas Bueno-de-Mesquita, Christina C. Dahm, Anne Kirstine Eriksen, Anne Tjønneland, Fanny Artaud, Marie Christine Boutron-Ruault, Gianluca Severi, Anika Hüsing, Antonia Trichopoulou, Anna Karakatsani, Eleni Peppa, Salvatore Panico, Giovanna Masala, Sara Grioni, Carlotta Sacerdote, Rosario Tumino, Sjoerd G. Elias, Anne M. May, Kristin Benjaminsen Borch, Torkjel M. Sandanger, Guri Skeie, María José Sánchez, José María Huerta, Núria Sala, Aurelio Barricarte Gurrea, J. Ramón Quiŕos, Pilar Amiano, Jonna Berntsson, Isabel Drake, Bethany Van Guelpen, Sophia Harlid, Tim Key, Elisabete Weiderpass, Elom K. Aglago, Amanda J. Cross, Konstantinos K. Tsilidis, Elio Riboli, Marc J. Gunter
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12943-021-01405-8

Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality
Cited by: 6
Author(s): Salvatore Benfatto, Özdemirhan Serçin, Francesca R. Dejure, Amir Abdollahi, Frank T. Zenke, Balca R. Mardin
Software Mentions: 9
Published: over 3 years ago

10.3390/v12111268

VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses
Cited by: 242
Author(s): Cristina Moraru, Arvind Varsani, Andrew M. Kropinski
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pbio.3000202

PlotsOfData—A web app for visualizing data together with their summaries
Cited by: 394
Author(s): Marten Postma, Joachim Goedhart
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41419-019-1775-y

A new bioavailable fenretinide formulation with antiproliferative, antimetabolic, and cytotoxic effects on solid tumors
Cited by: 34
Author(s): Isabella Orienti, Federica Francescangeli, Maria Laura De Angelis, Katia Fecchi, Lucilla Bongiorno-Borbone, Michele Signore, Angelo Peschiaroli, Alessandra Boe, Alessandro Bruselles, Angelita Costantino, Adriana Eramo, Valentina Salvati, Giovanni Sette, Paola Contavalli, Lello Zolla, Toshihiko Oki, Toshio Kitamura, Massimo Spada, Alessandro Giuliani, Marta Baiocchi, Filippo La Torre, Gerry Melino, Marco Tartaglia, Ruggero De Maria, Ann Zeuner
Software Mentions: 9
Published: over 5 years ago

10.1186/s13073-021-00902-1

Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer
Cited by: 16
Author(s): Corinna Keup, Vinay Suryaprakash, Siegfried Hauch, Markus Storbeck, Peter F. Hahn, Markus Sprenger-Haussels, Hans‐Christian Kolberg, Mitra Tewes, Oliver Hoffmann, Rainer Kimmig, Sabine Kasimir‐Bauer
Software Mentions: 9
Published: over 3 years ago

10.1093/gigascience/gix119

funRiceGenes dataset for comprehensive understanding and application of rice functional genes
Cited by: 69
Author(s): Wen Yao, Guangwei Li, Yiming Yu, Yidan Ouyang
Software Mentions: 9
Published: about 7 years ago

10.1038/s41598-020-76603-3

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots
Cited by: 230
Author(s): Joachim Goedhart, Martijn S. Luijsterburg
Software Mentions: 9
Published: about 4 years ago

10.1186/s12859-019-3105-x

MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
Cited by: 190
Author(s): Valerio Licursi, Federica Conte, Giulia Fiscon, Paola Paci
Software Mentions: 8
Published: about 5 years ago

10.1002/cam4.3350

Individualized prediction of survival benefits from perioperative chemoradiotherapy for patients with resectable gastric cancer
Cited by: 2
Author(s): Keying Che, Fangcen Liu, Nan Wu, Liu Q, Ling Yuan, Jia Wei
Software Mentions: 8
Published: over 4 years ago

10.1172/jci.insight.130510

Asymmetric cell division promotes therapeutic resistance in glioblastoma stem cells
Cited by: 19
Author(s): Masahiro Hitomi, Anastasia Chumakova, Daniel J. Silver, Arnon Møldrup Knudsen, William Pontius, Shaun Murphy, Neha Anand, Bjarne Winther Kristensen, Justin D. Lathia
Software Mentions: 8
Published: almost 4 years ago

10.3389/fimmu.2021.749459

A Machine Learning Model to Predict the Triple Negative Breast Cancer Immune Subtype
Cited by: 24
Author(s): Zihao Chen, Maoli Wang, Rudy Leon De Wilde, Ruifa Feng, Mingqiang Su, Wenjie Shi
Software Mentions: 8
Published: over 3 years ago

10.1186/2193-1801-3-474

Rapid publication-ready MS-Word tables for one-way ANOVA
Cited by: 131
Author(s): Houssein Assaad, Lan Zhou, Raymond J. Carroll, Guoyao Wu
Software Mentions: 8
Published: over 10 years ago

10.1186/s40170-020-00220-x

Metabolite AutoPlotter - an application to process and visualise metabolite data in the web browser
Cited by: 18
Author(s): Matthias Pietzke, Alexei Vazquez
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pntd.0006862

Viridot: An automated virus plaque (immunofocus) counter for the measurement of serological neutralizing responses with application to dengue virus
Cited by: 89
Author(s): Leah C. Katzelnick, Ana Coello Escoto, Benjamin D. McElvany, Christian Chávez, Henrik Salje, Wensheng Luo, Isabel Rodríguez-Barraquer, Richard G. Jarman, Anna P. Durbin, Sean A. Diehl, Derek J. Smith, Stephen S. Whitehead, Derek A. T. Cummings
Software Mentions: 8
Published: about 6 years ago

10.1371/journal.pone.0188966

AMModels: An R package for storing models, data, and metadata to facilitate adaptive management
Cited by: 2
Author(s): Therese M. Donovan, Jonathan E. Katz
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0233282

Can we decode phonetic features in inner speech using surface electromyography?
Cited by: 8
Author(s): Ladislas Nalborczyk, Romain Grandchamp, Ernst H. W. Koster, Marcela Perrone‐Bertolotti, Hélène Lœvenbruck
Software Mentions: 7
Published: over 4 years ago

10.1186/s13046-019-1505-4

A pre-existing population of ZEB2+ quiescent cells with stemness and mesenchymal features dictate chemoresistance in colorectal cancer
Cited by: 54
Author(s): Federica Francescangeli, Paola Contavalli, Maria Laura De Angelis, Silvia Careccia, Michele Signore, Tobias Haas, Federico Salaris, Marta Baiocchi, Alessandra Boe, Alessandro Giuliani, Olga Tcheremenskaia, Alfredo Pagliuca, Ombretta Guardiola, Gabriella Minchiotti, Lidia Colace, Antonio Ciardi, Vito D’Andrea, Filippo La Torre, Jan Paul Medema, Ruggero De Maria, Ann Zeuner
Software Mentions: 7
Published: almost 5 years ago

10.3389/fped.2020.623184

Timing of Newborn Blood Collection Alters Metabolic Disease Screening Performance
Cited by: 13
Author(s): Gang Peng, Yishuo Tang, Tina M. Cowan, Hongyu Zhao, Curt Scharfe
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12859-021-04392-1

shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study
Cited 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

10.12688/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

10.1371/journal.pone.0124600

MLViS: A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and Development
Cited by: 36
Author(s): Selçuk Korkmaz, Gökmen Zararsız, Dinçer Göksülük
Software Mentions: 7
Published: over 9 years ago

10.3390/ijns6010016

Reducing False-Positive Results in Newborn Screening Using Machine Learning
Cited by: 27
Author(s): Gang Peng, Yishuo Tang, Tina M. Cowan, Gregory M. Enns, Hongyu Zhao, Curt Scharfe
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12967-020-02616-1

Immune landscape of periodontitis unveils alterations of infiltrating immunocytes and molecular networks-aggregating into an interactive web-tool for periodontitis related immune analysis and visualization
Cited by: 7
Author(s): Xiaoqi Zhang, Qingxuan Wang, Xinyu Yan, Yue Shan, Xing Lü, Minqi Li, Hu Long, Wenli Lai
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-020-60891-w

An atlas of evidence-based phenotypic associations across the mouse phenome
Cited by: 3
Author(s): Nobuhiko Tanaka, Hiroshi Masuya
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41597-020-00731-8

CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties
Cited 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: about 4 years ago

10.1002/jrsm.1428

The Kilim plot: A tool for visualizing network meta‐analysis results for multiple outcomes
Cited by: 15
Author(s): Michael Seo, Toshi A Furukawa, Areti Angeliki Veroniki, Toby Pillinger, Anneka Tomlinson, Georgia Salanti, Andrea Cipriani, Orestis Efthimiou
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.34408

The MR-Base platform supports systematic causal inference across the human phenome
Cited by: 2,864
Author(s): Gibran Hemani, Jie Zheng, Benjamin Elsworth, Kaitlin H Wade, Valeriia Haberland, Denis Baird, Charles Laurin, Stephen Burgess, Jack Bowden, Ryan Langdon, Vanessa Tan, James Yarmolinsky, Hashem A. Shihab, Nicholas J. Timpson, David M. Evans, Caroline L Relton, Richard M. Martin, George Davey Smith, Tom R. Gaunt, Philip Haycock
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0246663

An open-sourced, web-based application to analyze weekly excess mortality based on the Short-term Mortality Fluctuations data series
Cited by: 38
Author(s): László Németh, Dmitri A. Jdanov, Vladimir M. Shkolnikov
Software Mentions: 6
Published: almost 4 years ago

10.12688/f1000research.4680.2

shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R
Cited by: 96
Author(s): Jean Philippe Fortin, Elana J. Fertig, Kasper D. Hansen
Software Mentions: 6
Published: over 10 years ago

10.12688/f1000research.13934.2

shinySISPA: A web tool for defining sample groups using gene sets from multiple-omics data
Cited by: 0
Author(s): Bhakti Dwivedi, Jeanne Kowalski
Software Mentions: 6
Published: over 6 years ago

10.1101/2020.04.28.20083279

CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties
Cited 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

10.1186/s12936-017-2130-3

Towards malaria elimination in Savannakhet, Lao PDR: mathematical modelling driven strategy design
Cited by: 18
Author(s): Sai Thein Than Tun, Lorenz von Seidlein, Tiengkham Pongvongsa, Mayfong Mayxay, Sompob Saralamba, Shwe Sin Kyaw, Phetsavanh Chanthavilay, O. Celhay, Tran Dang Nguyen, Thu Nguyen-Anh Tran, Daniel M. Parker, Maciej F. Boni, Arjen M. Dondorp, Lisa J. White
Software Mentions: 6
Published: about 7 years ago

10.1186/s12885-019-5993-6

Dynamic prediction of long-term survival in patients with primary gastric diffuse large B-cell lymphoma: a SEER population-based study
Cited by: 10
Author(s): Ju‐Li Lin, Lin Ji, Ping Li, Jian‐Wei Xie, Jia-Bin Wang, Jun Lü, Qi‐Yue Chen, Long‐Long Cao, Chang‐Ming Huang, Chao‐Hui Zheng
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-72095-3

Quantification of colorimetric isothermal amplification on the smartphone and its open-source app for point-of-care pathogen detection
Cited by: 42
Author(s): Huynh Quoc Nguyen, Van Dan Nguyen, Hau Van Nguyen, Tae Seok Seo
Software Mentions: 6
Published: over 4 years ago

10.3390/cancers12051084

Multimodal Targeted Deep Sequencing of Circulating Tumor Cells and Matched Cell-Free DNA Provides a More Comprehensive Tool to Identify Therapeutic Targets in Metastatic Breast Cancer Patients
Cited by: 13
Author(s): Corinna Keup, Markus Storbeck, Siegfried Hauch, Peter F. Hahn, Markus Sprenger-Haussels, Oliver Hoffmann, Rainer Kimmig, Sabine Kasimir‐Bauer
Software Mentions: 5
Published: over 4 years ago

10.1093/database/bax080

Edaphostat: interactive ecological analysis of soil organism occurrences and preferences from the Edaphobase data warehouse
Cited by: 0
Author(s): Jonas Hausen, Björn Scholz-Starke, Ulrich Burkhardt, Stephan Lesch, Sebastian Rick, David J. Russell, Martina Roß-Nickoll, Andreas Schäffer
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0226397

An open-sourced, web-based application to improve our ability to understand hunter and angler purchasing behavior from license data
Cited by: 0
Author(s): Nathaniel B. Price, Christopher J. Chizinski, Joseph J. Fontaine, Kevin L. Pope, Micaela Rahe, J. Rawlinson
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2017.00919

BSocial: Deciphering Social Behaviors within Mixed Microbial Populations
Cited by: 6
Author(s): Jessica Purswani, Rocío Romero-Záliz, Antonio Manuel Martín-Platero, Isabel M. Guisado, Jesús González‐López, Clementina Pozo
Software Mentions: 5
Published: over 7 years ago

10.1186/s13029-017-0063-4

DEApp: an interactive web interface for differential expression analysis of next generation sequence data
Cited by: 63
Author(s): Yan Li, Jorge Andrade
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0163711

hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine
Cited by: 7
Author(s): Steffen Falgreen, Anders Ellern Bilgrau, Rasmus Froberg Brøndum, Lasse Hjort Jakobsen, Jonas Have, Kasper Lindblad Nielsen, Tarec Christoffer El‐Galaly, Julie Støve Bødker, Alexander Schmitz, Ken H. Young, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted
Software Mentions: 5
Published: about 8 years ago

10.1093/gigascience/giz057

Map and model—moving from observation to prediction in toxicogenomics
Cited by: 15
Author(s): Andreas Schüttler, Rolf Altenburger, Madeleine Ammar, Marcella Bader-Blukott, Gianina Jakobs, Johanna Knapp, Janet Krüger, Kristin Reiche, Gi‐Mick Wu, Wibke Busch
Software Mentions: 5
Published: over 5 years ago

10.3390/jcm10173888

A Machine Learning Predictive Model for Post-Ureteroscopy Urosepsis Needing Intensive Care Unit Admission: A Case–Control YAU Endourology Study from Nine European Centres
Cited by: 16
Author(s): Amelia Pietropaolo, Robert Geraghty, Rajan Veeratterapillay, Alistair Rogers, Panagiotis Kallidonis, Luca Villa, Luca Boeri, Emanuele Montanari, Gökhan Atış, Esteban Emiliani, Tarık Emre Şener, Feras Al Jaafari, John Fitzpatrick, Matthew B.K. Shaw, Chris Harding, Bhaskar K. Somani
Software Mentions: 5
Published: over 3 years ago

10.3389/fvets.2020.558409

Socially vs. Privately Optimal Control of Livestock Diseases: A Case for Integration of Epidemiology and Economics
Cited by: 5
Author(s): Ângelo Mendes, Daniel T. Haydon, Emma McIntosh, Nick Hanley, Jo E.B. Halliday
Software Mentions: 5
Published: about 4 years ago

10.3389/fpls.2020.511768

R/UAStools::plotshpcreate: Create Multi-Polygon Shapefiles for Extraction of Research Plot Scale Agriculture Remote Sensing Data
Cited by: 14
Author(s): Steven L. Anderson, Seth C. Murray
Software Mentions: 5
Published: about 4 years ago

10.1093/hmg/ddz043

PAX7 target gene repression is a superior FSHD biomarker than DUX4 target gene activation, associating with pathological severity and identifying FSHD at the single-cell level
Cited by: 39
Author(s): Christopher R. S. Banerji, Peter S. Zammit
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2021.620002

AMRmap: An Interactive Web Platform for Analysis of Antimicrobial Resistance Surveillance Data in Russia
Cited by: 24
Author(s): Alexey Yu. Kuzmenkov, Ivan V. Trushin, Alina G. Vinogradova, Andrey A. Avramenko, М В Сухорукова, Surbhi Malhotra-Kumar, А В Дехнич, Mikhail V. Edelstein, Roman Kozlov
Software Mentions: 4
Published: almost 4 years ago

10.1038/s42003-021-02550-y

Composite trait Mendelian randomization reveals distinct metabolic and lifestyle consequences of differences in body shape
Cited by: 10
Author(s): Jonathan Sulc, Anthony Sonrel, Ninon Mounier, Chiara Auwerx, Eirini Marouli, Liza Darrous, Bogdan Draganski, Tuomas O. Kilpeläinen, Peter K. Joshi, Ruth J.F. Loos, Zoltán Kutalik
Software Mentions: 4
Published: over 3 years ago

10.1093/database/baz083

Phytochelatin database: a resource for phytochelatin complexes of nutritional and environmental metals
Cited by: 19
Author(s): Kristine K. Dennis, Karan Uppal, Ken H. Liu, Chunyu Ma, Bill Liang, Young‐Mi Go, Dean P. Jones
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1007253

Large-scale profiling of noncoding RNA function in yeast
Cited by: 25
Author(s): Steven J. Parker, Marcin G. Fraczek, Jian Wu, Sara Shamsah, Alkisti Manousaki, Kobchai Dungrattanalert, Rogério Alves de Almeida, Edith Invernizzi, Tim Burgis, Walid Omara, Sam Griffiths-Jones, Daniela Delneri, Raymond T. O’Keefe
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13071-020-04114-1

The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level
Cited by: 12
Author(s): Antoine Mignotte, Claire Garros, Laëtitia Gardès, Thomas Balenghien, Maxime Duhayon, Ignace Rakotoarivony, Laura Tabourin, Léa Poujol, Bruno Mathieu, Adolfo Ibáñez-Justicia, Ahmet Deniz, Aleksandar Cvetkovikj, Bethan V. Purse, David W. Ramilo, Despoina Stougiou, Doreen Werner, Dubravka Pudar, Dušan Petrić, Eva Veronesi, Frans Jacobs, Helge Kampen, Isabel Pereira da Fonseca, Javier Lucientes, J. Nelson Navarro, Josué Martínez de la Puente, Jovana Stefanovska, Kate R. Searle, Khalid Khallaayoune, C. Lorna Culverwell, Magdalena Larska, Maria Bourquia, Maria Goffredo, Marina Bisia, Marion England, Matthew Robin, Michela Quaglia, Miguel Ángel Miranda, René Bødker, Rosa Estrada-Peña, Simon Carpenter, Simona Tchakarova, Sofia Boutsini, Ståle Sviland, Stefanie Schäfer, Zanda Ozoliņa, Zanda Segliņa, Zati Vatansever, Karine Huber
Software Mentions: 4
Published: over 4 years ago

10.1186/s12957-020-02061-w

Development of prognosis model for colon cancer based on autophagy-related genes
Cited by: 9
Author(s): Xu Wang, Yihang Xu, Ting Li, Bin Chen, Wei Yang
Software Mentions: 4
Published: about 4 years ago

10.12688/f1000research.15789.2

TRGAted: A web tool for survival analysis using protein data in the Cancer Genome Atlas.
Cited by: 18
Author(s): Nicholas Borcherding, Nicholas L. Bormann, Andrew P. Voigt, Weizhou Zhang
Software Mentions: 4
Published: about 6 years ago

10.1186/s12936-018-2203-y

Insecticide resistance evolution with mixtures and sequences: a model-based explanation
Cited by: 31
Author(s): Andy South, Ian M. Hastings
Software Mentions: 4
Published: almost 7 years ago

10.3389/fonc.2020.01658

Circulating Tumor Cells Expressing the Prostate Specific Membrane Antigen (PSMA) Indicate Worse Outcome in Primary, Non-Metastatic Triple-Negative Breast Cancer
Cited by: 14
Author(s): Sabine Kasimir‐Bauer, Corinna Keup, Oliver Hoffmann, Siegfried Hauch, Rainer Kimmig, Ann‐Kathrin Bittner
Software Mentions: 4
Published: over 4 years ago

10.3389/fonc.2020.582567

Development and Validation of a Novel Risk Stratification Model for Cancer-Specific Survival in Diffuse Large B-Cell Lymphoma
Cited by: 5
Author(s): Qun Zhong, Yuankai Shi
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12889-021-10961-z

Real time surveillance of COVID-19 space and time clusters during the summer 2020 in Spain
Cited by: 171
Author(s): Nicolás Rosillo, Javier Del-Águila-Mejía, Ayelén Rojas-Benedicto, María Guerrero-Vadillo, Marina Peñuelas, Clara Mazagatos, Jordi Segú-Tell, Rebeca Ramis, Diana Gómez-Barroso
Software Mentions: 4
Published: over 3 years ago

10.1128/mBio.02259-20

Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments
Cited by: 18
Author(s): Madeline Tong, Shawn French, Sara S. El Zahed, Wai Kit Ong, Peter D. Karp, Eric D. Brown
Software Mentions: 4
Published: about 4 years ago

Projects: cran: shiny

Papers Mentioning shiny 127