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: io
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/io
A Unified Framework for Input-Output Operations in R
8 versions
Latest release: almost 5 years ago
1 dependent package
223 downloads last month
Papers Mentioning io 50
10.7717/peerj.453
scikit-image: image processing in PythonCited by: 3,381
Author(s): Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu
Software Mentions: 10
Published: over 10 years ago
10.1186/s12859-016-1003-z
Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulationsCited by: 26
Author(s): Niklaus Johner, Daniel Harries, George Khelashvili
Software Mentions: 8
Published: over 8 years ago
10.1186/s12859-019-2796-3
rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformaticsCited by: 15
Author(s): Jaume Bonet, Zander Harteveld, Fabian Sesterhenn, Andreas Scheck, Bruno E. Correia
Software Mentions: 7
Published: over 5 years ago
10.12688/f1000research.9618.2
biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) formatCited by: 2
Author(s): Markus J. Ankenbrand, Niklas Terhoeven, Sonja Hohlfeld, Frank Förster, Alexander Keller
Software Mentions: 7
Published: almost 8 years ago
10.1186/1756-0500-4-331
Agile parallel bioinformatics workflow management using PwrakeCited by: 20
Author(s): Hiroyuki Mishima, Kensaku Sasaki, M. Tanaka, Osamu Tatebe, Koh-ichiro Yoshiura
Software Mentions: 7
Published: about 13 years ago
10.1186/1471-2342-8-10
Internet Image Viewer (iiV)Cited by: 9
Author(s): Joel T. Lee, Kristin Munch, John V. Carlis, José V. Pardo
Software Mentions: 6
Published: over 16 years ago
10.1007/s10237-021-01520-x
Spatiotemporal modeling of first and second wave outbreak dynamics of COVID-19 in GermanyCited by: 10
Author(s): Dorothee Lippold, Andreas Kergaßner, Christian Burkhardt, Matthias Kergaßner, Jonas Loos, Sarah Nistler, Paul Steinmann, Dominik Budday, Silvia Budday
Software Mentions: 6
Published: about 3 years ago
10.1371/journal.pone.0244616
Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and IndonesiaCited by: 11
Author(s): Jan Niklas Macher, Martina Prazeres, Sarah Taudien, Jamaluddin Jompa, Aleksey Sadekov, Willem Renema
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pcbi.1002970
Chaste: An Open Source C++ Library for Computational Physiology and BiologyCited by: 366
Author(s): Gary R. Mirams, Christopher J. Arthurs, Miguel O. Bernabéu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G. Fletcher, Daniel G. Harvey, Megan E. Marsh, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Néjib Zemzemi, David Gavaghan
Software Mentions: 6
Published: over 11 years ago
10.3390/cells8121510
A New Sensitive Method for the Detection of Mycoplasmas Using Fluorescence MicroscopyCited by: 10
Author(s): Anna Ligasová, Markéta Vydržalová, Renata Buriánová, Lenka Brůčková, Renata Večeřová, Anna Janošťáková, Karel Koberna
Software Mentions: 5
Published: almost 5 years ago
10.7717/peerj-cs.232
On-demand virtual research environments using microservicesCited by: 10
Author(s): Marco Capuccini, Anders Larsson, Matteo Carone, Jon Ander Novella, Noureddin Sadawi, Jianliang Gao, Salman Toor, Ola Spjuth
Software Mentions: 5
Published: about 5 years ago
10.1371/journal.pone.0245710
Isolation of the Buchnera aphidicola flagellum basal body complexes from the Buchnera membraneCited by: 1
Author(s): Matthew J. Schepers, James N. Yelland, Nancy A. Moran, David W. Taylor
Software Mentions: 5
Published: over 3 years ago
10.1093/gigascience/giz067
Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-CCited by: 52
Author(s): Changming Bai, Lusheng Xin, Umberto Rosani, Biao Wu, Qingchen Wang, Xiaoke Duan, Zhihong Liu, Wang Chongming
Software Mentions: 4
Published: over 5 years ago
10.7150/jca.56506
Identification of Hub Genes and Small Molecule Drugs Associated with Acquired Resistance to Gefitinib in Non-Small Cell Lung CancerCited by: 8
Author(s): Guangda Li, You-Zhi Ma, Mingwei Yu, Xiaoxiao Li, Xinjie Chen, Yu Tang Gao, Pei-Yu Cheng, Gan‐Lin Zhang, Xiaomin Wang
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41597-020-0415-9
A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory taskCited by: 8
Author(s): Nand Chandravadia, Daan Liang, Andrea Gómez Palacio Schjetnan, April A Carlson, Maïlys C. M. Faraut, Jeffrey M. Chung, Chrystal M. Reed, Benjamin Dichter, Uri Maoz, Suneil K. Kalia, Taufik A. Valiante, Adam N. Mamelak, Ueli Rutishauser
Software Mentions: 4
Published: over 4 years ago
10.7717/peerj-cs.156
Comparison and benchmark of name-to-gender inference servicesCited by: 197
Author(s): L. Santamaría, Helena Mihaljević
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pcbi.1009227
Relating simulation studies by provenance—Developing a family of Wnt signaling modelsCited by: 5
Author(s): Kai Budde, Jacob Smith, Pia Wilsdorf, Fiete Haack, Adelinde M. Uhrmacher
Software Mentions: 4
Published: over 3 years ago
10.12688/f1000research.9453.2
Method-centered digital communities on protocols.io for fast-paced scientific innovationCited by: 0
Author(s): Lori Kindler, Alexei Stoliartchouk, Leonid Teytelman, Bonnie Hurwitz
Software Mentions: 4
Published: over 7 years ago
10.3389/fnhum.2021.713114
Visual Field Reconstruction in Hemianopia Using fMRI Based Mapping TechniquesCited by: 1
Author(s): Hinke N. Halbertsma, Holly Bridge, Joana Carvalho, Frans W. Cornelissen, Sara Ajina
Software Mentions: 4
Published: over 3 years ago
10.3389/fnins.2018.00006
Group Analysis in MNE-Python of Evoked Responses from a Tactile Stimulation Paradigm: A Pipeline for Reproducibility at Every Step of Processing, Going from Individual Sensor Space Representations to an across-Group Source Space RepresentationCited by: 17
Author(s): Lau M. Andersen
Software Mentions: 4
Published: almost 7 years ago
10.1186/s12879-021-06586-7
Antibody seroprevalence and rate of asymptomatic infections with SARS-CoV-2 in Austrian hospital personnelCited by: 3
Author(s): Iris Leister, Elisabeth Ponocny‐Seliger, Herwig Kollaritsch, Peter Dungel, Barbara Holzer, Johannes Grillari, Heinz Redl, Ivo Ponocny, Claudia Wilfing, Ludwig Aigner, Markus Exner, Michaela Stainer, Matthias Hackl, T. Hausner, Rainer Mittermayr, Wolfgang Schaden
Software Mentions: 4
Published: about 3 years ago
10.2196/resprot.8397
Influence of Information and Communication Technologies on the Resilience and Coping of Sexual and Gender Minority Youth in the United States and Canada (Project #Queery): Mixed Methods SurveyCited by: 30
Author(s): Shelley L. Craig, Lauren B. McInroy, Sandra D'Souza, Ashley Austin, Lance T. McCready, Andrew Eaton, Leslie Regan Shade, M. Alex Wagaman
Software Mentions: 3
Published: about 7 years ago
10.12688/f1000research.10137.1
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflowsCited by: 83
Author(s): Brian D. O’Connor, Denis Yuen, Vincent Chung, A. Duncan, Xiang Kun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
Software Mentions: 3
Published: almost 8 years ago
10.1093/gigascience/gix066
Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detectionCited by: 9
Author(s): Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lü, Xiaosen Guo, Guibo Li, Yong Hou, Shi Ping Liu, Bo Li
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pbio.2004956
The gender gap in science: How long until women are equally represented?Cited by: 423
Author(s): Luke Holman, Devi Stuart‐Fox, Cindy E. Hauser
Software Mentions: 3
Published: over 6 years ago
10.1093/gigascience/giaa070
Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheatCited by: 19
Author(s): Fu-Hao Lu, Neil McKenzie, Laura‐Jayne Gardiner, Ming Luo, Anthony Hall, Michael W. Bevan
Software Mentions: 3
Published: over 4 years ago
10.3389/fneur.2018.00684
Thigh-Derived Inertial Sensor Metrics to Assess the Sit-to-Stand and Stand-to-Sit Transitions in the Timed Up and Go (TUG) Task for Quantifying Mobility Impairment in Multiple SclerosisCited by: 27
Author(s): Harry J. Witchel, Cäcilia Oberndorfer, Robert Needham, Aoife Healy, Carina E. I. Westling, Joseph H. Guppy, Jake Bush, Jens Barth, Chantal Herberz, Daniel Roggen, Bjoern M. Eskofier, Waqar Rashid, Nachiappan Chockalingam, Jochen Klucken
Software Mentions: 3
Published: about 6 years ago
10.1093/gigascience/giz007
Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical GardenCited by: 36
Author(s): Huan Liu, Jinpu Wei, Ting Yang, Weixue Mu, Bo Song, Tuo Yang, Yuan Fang, Xuebing Wang, Guohai Hu, Wangsheng Li, Hong Zhou, Xiaoli Chen, Hongyun Chen, Lei Cheng, Xiao Shun He, Hechen Cai, Xianchu Cai, Mei Wang, Yang Li, Sunil Kumar Sahu, Jing Yang, Yu Wang, Ranchang Mu, Jie Liu, Jianming Zhao, Ziheng Huang, Xun Xu, Xin Liu
Software Mentions: 3
Published: almost 6 years ago
10.3389/fphys.2021.627088
Poincaré Plot Area of Gamma-Band EEG as a Measure of Emergence From Inhalational General AnesthesiaCited by: 5
Author(s): Kazuma Hayase, Atsushi Kainuma, Koichi Akiyama, Mao Kinoshita, Masayuki Shibasaki, Teiji Sawa
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13326-016-0111-z
Consolidating drug data on a global scale using Linked DataCited by: 20
Author(s): Milos Jovanovik, Dimitar Trajanov
Software Mentions: 3
Published: almost 8 years ago
10.1200/CCI.19.00110
Exploring Integrative Analysis Using the BioMedical Evidence GraphCited by: 4
Author(s): Adam J. Struck, Brian Walsh, Alexander Buchanan, Jordan A. Lee, Ryan Spangler, Joshua M. Stuart, Kyle Ellrott
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0246167
Evidence and magnitude of the effects of meteorological changes on SARS-CoV-2 transmissionCited by: 12
Author(s): Adam I. Kaplin, Caesar Junker, Anupama Kumar, Mary Anne Ribeiro, Eileen Yu, Michael Wang, Ted Smith, N. Shesh, Aruni Bhatnagar
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0257643
Geographical variation in demand, utilization, and outcomes of hospital services for COVID-19 in Brazil: A descriptive serial cross-sectional studyCited by: 7
Author(s): Claudia Cristina de Aguiar Pereira, Mônica Martins, Sheyla Maria Lemos Lima, Carla Lourenço Tavares de Andrade, Fernando Ramalho Gameleira Soares, Margareth Crisóstomo Portela
Software Mentions: 3
Published: about 3 years ago
10.1371/journal.pone.0234354
Negshell casting: 3D-printed structured and sacrificial cores for soft robot fabricationCited by: 5
Author(s): Pornthep Preechayasomboon, Eric Rombokas
Software Mentions: 3
Published: over 4 years ago
10.5195/jmla.2021.1185
Performance of gender detection tools: a comparative study of name-to-gender inference servicesCited by: 47
Author(s): Paul Sebo
Software Mentions: 3
Published: about 3 years ago
10.2196/17496
A Social Media Study on the Associations of Flavored Electronic Cigarettes With Health Symptoms: Observational StudyCited by: 30
Author(s): Long Chen, Xinyi Lu, Jianbo Yuan, Joyce Luo, Jiebo Luo, Zidian Xie, Dongmei Li
Software Mentions: 2
Published: over 4 years ago
10.15252/msb.20188556
Structured Methods for reproducible scienceCited by: 1
Author(s): Maria Polychronidou
Software Mentions: 2
Published: over 6 years ago
10.1007/s10055-021-00585-4
Harmonize: a shared environment for extended immersive entertainmentCited by: 6
Author(s): Damiano Oriti, Federico Manuri, Francesco De Pace, Andrea Sanna
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pbio.1002538
Protocols.io: Virtual Communities for Protocol Development and DiscussionCited by: 42
Author(s): Lenny Teytelman, Alexei Stoliartchouk, Lori Kindler, Bonnie Hurwitz
Software Mentions: 2
Published: over 8 years ago
10.3389/fendo.2021.662769
Brain-Body Control of Glucose Homeostasis—Insights From Model OrganismsCited by: 4
Author(s): Alastair Macdonald, Yu Hsuan Carol Yang, Cruz Am, Craig Beall, Kate L. J. Ellacott
Software Mentions: 2
Published: over 3 years ago
10.1093/gigascience/gix064
Looking back: forward lookingCited by: 2
Author(s): Scott Edmunds, Nicole Nogoy, Hans Zauner, Peter Li, Chris Hunter, Sizhe Xiao, Laurie Goodman
Software Mentions: 2
Published: over 7 years ago
10.1093/gigascience/gix067
Deep whole-genome sequencing of 90 Han Chinese genomesCited by: 35
Author(s): Tianming Lan, Haoxiang Lin, Wenjuan Zhu, Tellier Christian Asker Melchior Laurent, Mofeng Yang, Xin Liu, Jun Wang, Jian Wang, Huanming Yang, Xun Xu, Xiaosen Guo
Software Mentions: 2
Published: over 7 years ago
10.1093/gigascience/gix047
The metagenomic data life-cycle: standards and best practicesCited by: 36
Author(s): Petra ten Hoopen, Alex Bateman, Lars Ailo Bongo, Matthieu Le Corre, Bruno Fosso, Folker Meyer, Alex L. Mitchell, Éric Pelletier, Graziano Pesole, Mónica Santamaría, Nils Peder Willassen, Guy Cochrane
Software Mentions: 2
Published: over 7 years ago
10.1093/gigascience/giz127
Key challenges facing data-driven multicellular systems biologyCited by: 31
Author(s): Paul Macklin
Software Mentions: 2
Published: about 5 years ago
10.1128/JCM.00876-20
Open Development and Clinical Validation of Multiple 3D-Printed Nasopharyngeal Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing BottleneckCited by: 93
Author(s): Cody Callahan, Rose Lee, Katelyn E. Zulauf, Lauren Tamburello, Kenneth P. Smith, Joe Previtera, Annie Cheng, Alexander L. Green, Ahmed Abdul Azim, Amanda Yano, Nancy Doraiswami, James E. Kirby, Ramy Arnaout
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-021-81767-7
Topological impact of negative links on the stability of resting-state brain networkCited by: 24
Author(s): Majid Saberi, Reza Khosrowabadi, Ali Khatibi, Bratislav Mišić, G. R. Jafari
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-021-85602-x
White matter alterations in glaucoma and monocular blindness differ outside the visual systemCited by: 12
Author(s): Sandra Hanekamp, Branislava Ćurčić‐Blake, Bradley Caron, Brent McPherson, Anneleen Timmer, Doety Prins, Christine C. Boucard, Masaki Yoshida, Masahiro Ida, David Hunt, Nomdo M. Jansonius, Franco Pestilli, Frans W. Cornelissen
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-021-96707-8
AI outperformed every dermatologist in dermoscopic melanoma diagnosis, using an optimized deep-CNN architecture with custom mini-batch logic and loss functionCited by: 27
Author(s): Tri-Cong Pham, Chi-Mai Luong, Vu Hoang, Antoine Doucet
Software Mentions: 2
Published: about 3 years ago
10.3390/s17071513
Analysis of Public Datasets for Wearable Fall Detection SystemsCited by: 96
Author(s): E. Casilari, José Antonio Santoyo-Ramón, José Manuel Cano-García
Software Mentions: 2
Published: over 7 years ago
10.3390/s20215969
Towards a Safer Internet of Things—A Survey of IoT Vulnerability Data SourcesCited by: 13
Author(s): Marcin Rytel, Anna Felkner, Marek Janiszewski
Software Mentions: 2
Published: about 4 years ago