pypi: github | Projects | Ecosyste.ms: Papers

10.12688/f1000research.8986.2

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: over 7 years ago

10.12688/f1000research.7082.3

EvolQG - An R package for evolutionary quantitative genetics
Cited by: 31
Author(s): Diogo Melo, Guilherme Garcia, Alex Hubbe, Ana Paula A. Assis, Gabriel Marroig
Software Mentions: 13
Published: over 7 years ago

10.7554/eLife.62587

Selfing is the safest sex for Caenorhabditis tropicalis
Cited by: 30
Author(s): Luke M. Noble, John G Yuen, Lewis Stevens, Nicolas Moya, Riaad Persaud, Marc Moscatelli, Jacqueline L. Jackson, Gaotian Zhang, Rojin Chitrakar, L. Ryan Baugh, Christian Braendle, Erik C. Andersen, Hannah S. Seidel, Matthew V. Rockman
Software Mentions: 13
Published: over 3 years ago

10.12688/f1000research.7118.2

DREAMTools: a Python package for scoring collaborative challenges
Cited by: 9
Author(s): Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Alberto de la Fuente, Mehmet Gönen, Steven M. Hill, Bruce Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden, Pablo Meyer, Raquel Norel, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello, Gustavo Stolovitzky, Julio Sáez-Rodríguez
Software Mentions: 10
Published: about 8 years ago

10.1371/journal.pcbi.1008748

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Cited by: 6
Author(s): Martín Garrido‐Rodriguez, Daniel López-López, Francisco Ortuño, María Peña‐Chilet, Eduardo Muñóz, Marco A. Calzado, Joaquı́n Dopazo
Software Mentions: 8
Published: over 3 years ago

10.12688/f1000research.12974.1

Using bio.tools to generate and annotate workbench tool descriptions
Cited by: 8
Author(s): Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Helena Rasche, Michael R. Crusoe, Hedi Peterson, Jon C. Ison, Hervé Ménager
Software Mentions: 8
Published: over 6 years ago

10.7554/eLife.31035

Phenotype inference in an Escherichia coli strain panel
Cited by: 36
Author(s): Marco Galardini, Alexandra Koumoutsi, Lucía Herrera-Domínguez, Juan Antonio Cordero Varela, Anja Telzerow, Omar Wagih, Morgane Wartel, Olivier Clermont, Erick Denamur, Athanasios Typas, Pedro Beltrão
Software Mentions: 8
Published: over 6 years ago

10.3389/fninf.2016.00027

CoSMoMVPA: Multi-Modal Multivariate Pattern Analysis of Neuroimaging Data in Matlab/GNU Octave
Cited by: 386
Author(s): Nikolaas N. Oosterhof, Andrew C. Connolly, James V. Haxby
Software Mentions: 7
Published: almost 8 years ago

10.1038/s41597-020-00760-3

Data-science ready, multisite, human diffusion MRI white-matter-tract statistics
Cited by: 9
Author(s): Garikoitz Lerma-Usabiaga, Pratik Mukherjee, Mike Perry, Brian A. Wandell
Software Mentions: 7
Published: over 3 years ago

10.7717/peerj.5853

BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
Cited by: 3
Author(s): Jianfeng Li, Bowen Cui, Yuting Dai, Lijun Bai, Huang Jy
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj-cs.601

GrimoireLab: A toolset for software development analytics
Cited by: 16
Author(s): Santiago Dueñas, Valerio Cosentino, Jesús M. González-Barahona, Alvaro del Castillo San Félix, Daniel Izquierdo-Cortázar, Luis Cañas-Díaz, Alberto Pérez García-Plaza
Software Mentions: 6
Published: almost 3 years ago

10.1371/journal.pone.0239021

Estimating the effect of a scanner upgrade on measures of grey matter structure for longitudinal designs
Cited by: 8
Author(s): Evelyn Medawar, Ronja Thieleking, Iryna Manuilova, Maria Paerisch, Arno Villringer, A. Veronica Witte, Frauke Beyer
Software Mentions: 6
Published: over 2 years ago

10.1371/journal.pcbi.1007786

Minimizing the number of optimizations for efficient community dynamic flux balance analysis
Cited by: 12
Author(s): James D. Brunner, Nicholas Chia
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0241231

A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica
Cited by: 7
Author(s): Joel H. Nitta, Atsushi Ebihara, Alan Р. Smith
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.62719

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain
Cited by: 14
Author(s): Michael Sheinman, Ksenia Arkhipova, Peter F. Arndt, Bas E. Dutilh, Rutger Hermsen, Florian Massip
Software Mentions: 5
Published: almost 3 years ago

10.1371/journal.pbio.3000959

The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape
Cited by: 219
Author(s): Nicholas Fraser, Liam Brierley, G.K. Dey, Jessica Polka, Máté Pálfy, Federico Nanni, Jonathan Coates
Software Mentions: 5
Published: about 3 years ago

10.1038/sdata.2019.30

Assessing data availability and research reproducibility in hydrology and water resources
Cited by: 56
Author(s): James H. Stagge, David E. Rosenberg, Adel M. Abdallah, Hadia Akbar, Nour A. Attallah, R.W. James
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1009697

A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics
Cited by: 27
Author(s): Geyu Zhou, Hongyu Zhao
Software Mentions: 5
Published: almost 3 years ago

10.1186/1471-2105-12-S15-S5

Data hosting infrastructure for primary biodiversity data
Cited by: 13
Author(s): Anthony Goddard, Nevin Wilson, Phil Cryer, Grant Yamashita
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pone.0252457

Lack of parent-of-origin effects in Nasonia jewel wasp: A replication and extension study
Cited by: 1
Author(s): Kimberly C. Olney, Joshua D. Gibson, Heini M. Natri, Avery Underwood, Juergen Gadau, Melissa A. Wilson
Software Mentions: 5
Published: almost 3 years ago

10.1371/journal.pone.0249899

A pseudomolecule assembly of the Rocky Mountain elk genome
Cited by: 2
Author(s): Rick E. Masonbrink, David P. Alt, Darrell O. Bayles, Paola M. Boggiatto, William H. Edwards, Fred M. Tatum, Jeffrey T. Williams, Jennifer H. Wilson-Welder, Aleksey V. Zimin, Andrew J. Severin, Steven C. Olsen
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0227161

Assessing trends and vulnerabilities in the mutualism between whitebark pine (Pinus albicaulis) and Clark’s nutcracker (Nucifraga columbiana) in national parks of the Sierra-Cascade region
Cited by: 2
Author(s): Chris Ray, Regina M. Rochefort, Jason I. Ransom, Jonathan C. B. Nesmith, Sylvia Haultain, Taza D. Schaming, John R. Boetsch, Mandy L Holmgren, Robert L. Wilkerson, Rodney B. Siegel
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0231510

Analyses of cancer incidence and other morbidities in gamma irradiated B6CF1 mice
Cited by: 7
Author(s): Alia Zander, Tatjana Paunesku, Gayle E. Woloschak
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pcbi.1008647

Independent component analysis recovers consistent regulatory signals from disparate datasets
Cited by: 24
Author(s): Anand V. Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol Kavvas, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0249695

Use of amplicon-based sequencing for testing fetal identity and monogenic traits with Single Circulating Trophoblast (SCT) as one form of cell-based NIPT
Cited by: 5
Author(s): Xinming Zhuo, Qun Wang, Liesbeth Vossaert, Roseen Salman, Adriel Kim, Ignatia Van den Veyver, Amy M. Breman, Arthur L. Beaudet
Software Mentions: 4
Published: about 3 years ago

10.1186/1471-2164-12-285

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence
Cited by: 56
Author(s): José Blanca, Laura Pascual, Peio Ziarsolo, F. Nuez
Software Mentions: 4
Published: about 13 years ago

10.1186/s12859-017-1615-y

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
Cited by: 16
Author(s): Garrett W. Birkel, Amit Ghosh, Vinay Satish Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling, Héctor García Martín
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.69698

Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision
Cited by: 18
Author(s): James A Watson, Carolyne Ndila, Sophie Uyoga, Alexander Macharia, Gideon Nyutu, Shebe Mohammed, Caroline Ngetsa, Neema Mturi, Norbert Peshu, Benjamin Tsofa, Kirk A. Rockett, Stije J. Leopold, Hugh Kingston, Elizabeth C. George, Kathryn Maitland, Nicholas P. J. Day, Arjen M. Dondorp, Philip Bejon, Thomas N. Williams, Chris Holmes, Nicholas J. White
Software Mentions: 3
Published: almost 3 years ago

10.1371/journal.pcbi.1008266

A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors
Cited by: 8
Author(s): Juan Jiménez-Sánchez, Álvaro Martínez-Rubio, Антон Попов, Julián Pérez-Beteta, Youness Azimzade, David Molina-García, Juan Belmonte-Beitia, Gabriel F. Calvo, Víctor M. Pérez‐García
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0252775

The role of state feelings of loneliness in the situational regulation of social affiliative behavior: Exploring the regulatory relations within a multilevel framework
Cited by: 5
Author(s): Andreas Reißmann, Ewelina Stollberg, Joachim Hauser, Ivo Kaunzinger, Klaus W. Lange
Software Mentions: 3
Published: almost 3 years ago

10.1371/journal.pone.0226428

GLAMbox: A Python toolbox for investigating the association between gaze allocation and decision behaviour
Cited by: 7
Author(s): Felix Molter, Armin W. Thomas, Hauke R. Heekeren, Peter N. C. Mohr
Software Mentions: 3
Published: over 4 years ago

10.12688/f1000research.27214.2

iCAT: diagnostic assessment tool of immunological history using high-throughput T-cell receptor sequencing
Cited by: 2
Author(s): Ahmad Rajeh, Kyle J. Wolf, Courtney Schiebout, Nabeel Sait, Tim Kosfeld, Richard J. DiPaolo, Tae-Hyuk Ahn
Software Mentions: 3
Published: almost 3 years ago

10.1038/s41598-018-35218-5

Machine learning based classification of cells into chronological stages using single-cell transcriptomics
Cited by: 16
Author(s): Sumeet Pal Singh, Sharan Janjuha, Samata Chaudhuri, Susanne Reinhardt, Annekathrin Kränkel, Sevina Dietz, Anne Eugster, Halil I. Bilgin, Selçuk Korkmaz, Gökmen Zararsız, Nikolay Ninov, John E. Reid
Software Mentions: 3
Published: over 5 years ago

10.1186/s40064-016-2897-7

Influence analysis of Github repositories
Cited by: 35
Author(s): Yan Hu, Jun Zhang, Xiaomei Bai, Shuo Yu, Zaiyou Yang
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.46923

Consistent and correctable bias in metagenomic sequencing experiments
Cited by: 245
Author(s): Michael R. McLaren, Amy Willis, Benjamin J. Callahan
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0227730

Extracting lung function measurements to enhance phenotyping of chronic obstructive pulmonary disease (COPD) in an electronic health record using automated tools
Cited by: 9
Author(s): Kathleen M. Akgün, Keith Sigel, Kei‐Hoi Cheung, Farah Kidwai-Khan, Alex K. Bryant, Cynthia Brandt, Amy C. Justice, Kristina Crothers
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.44491

Primed Track, high-fidelity lineage tracing in mouse pre-implantation embryos using primed conversion of photoconvertible proteins
Cited by: 3
Author(s): Maaike Welling, Manuel Mohr, Aaron Ponti, Lluc Rullan Sabater, Andrea Boni, Yuuki Kawamura, Prisca Liberali, Antoine H.F.M. Peters, Paweł Pelczar, Periklis Pantazis
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1007406

Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila
Cited by: 3
Author(s): Sebastian M. Bernasek, Nicolás Peláez, Richard W. Carthew, Neda Bagheri, Luı́s A. Nunes Amaral
Software Mentions: 2
Published: over 4 years ago

10.3390/metabo10080327

VenoMS—A Website for the Low Molecular Mass Compounds in Spider Venoms
Cited by: 7
Author(s): Yvonne Forster, Silvan Reusser, Florian Forster, Stefan Bienz, Laurent Bigler
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pcbi.1009383

A unified mechanism for innate and learned visual landmark guidance in the insect central complex
Cited by: 21
Author(s): Roman Goulard, Cornelia Buehlmann, Paul Graham, Barbara Webb
Software Mentions: 2
Published: over 2 years ago

10.7554/eLife.58631

Concentration-dependent mortality of chloroquine in overdose
Cited by: 20
Author(s): James A Watson, Joel Tärning, Richard M Hoglund, Frédéric J. Baud, Bruno Mégarbane, Jean Luc Clemessy, Nicholas J. White
Software Mentions: 2
Published: almost 4 years ago

10.3390/metabo11050300

IDARE2—Simultaneous Visualisation of Multiomics Data in Cytoscape
Cited by: 2
Author(s): Thomas Pfau, Mafalda Galhardo, Jake Lin, Thomas Sauter
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0250106

Effects of raster terrain representation on GIS shortest path analysis
Cited by: 5
Author(s): F. Antonio Medrano
Software Mentions: 2
Published: about 3 years ago

10.1155/2021/8890226

Deep Ensemble Model for Classification of Novel Coronavirus in Chest X-Ray Images
Cited by: 38
Author(s): Fadzil Ahmad, Amjad Farooq, Muhammad Usman Ghani
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1008642

Health inequities in influenza transmission and surveillance
Cited by: 18
Author(s): Casey M. Zipfel, Vittoria Colizza, Shweta Bansal
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0242127

COVID-19 in-hospital mortality and mode of death in a dynamic and non-restricted tertiary care model in Germany
Cited by: 48
Author(s): Siegbert Rieg, Maja von Cube, Johannes Kalbhenn, Stefan Utzolino, Katharina Pernice, Lena Bechet, Johanna Baur, Corinna N. Lang, Dirk Wagner, Martin Wolkewitz, Winfried V. Kern, Paul Biever
Software Mentions: 2
Published: over 3 years ago

10.12688/f1000research.6139.3

MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data
Cited by: 1
Author(s): Damien Correia, Olivia Doppelt-Azeroual, Jean-Baptiste Denis, Mathias Vandenbogaert, Valérie Caro
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.28629

Inferring genetic interactions from comparative fitness data
Cited by: 30
Author(s): Kristina Crona, Alex Gavryushkin, Devin Greene, Niko Beerenwinkel
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0181570

Graphettes: Constant-time determination of graphlet and orbit identity including (possibly disconnected) graphlets up to size 8
Cited by: 9
Author(s): Adib Hasan, Po-Chien Chung, Wayne B. Hayes
Software Mentions: 1
Published: almost 7 years ago

10.1371/currents.tol.bf01eff4a6b60ca4825c69293dc59645

Best Practices for Data Sharing in Phylogenetic Research
Cited by: 17
Author(s): Karen Cranston, Luke J. Harmon, Maureen A. O’Leary, Curtis Lisle
Software Mentions: 1
Published: over 10 years ago

10.3389/fncom.2015.00030

A long journey into reproducible computational neuroscience
Cited by: 23
Author(s): Meropi Topalidou, Arthur Leblois, Thomas Boraud, Nicolas P. Rougier
Software Mentions: 1
Published: about 9 years ago

10.1186/1758-2946-3-36

Openness as infrastructure
Cited by: 6
Author(s): John Wilbanks
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-018-28706-1

The influenza virus hemagglutinin head evolves faster than the stalk domain
Cited by: 160
Author(s): Ericka Kirkpatrick, Xueting Qiu, Patrick C. Wilson, Justin Bahl, Florian Krammer
Software Mentions: 1
Published: almost 6 years ago

10.7554/eLife.32563

TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response
Cited by: 25
Author(s): Dmitry E. Andreev, Maxim Arnold, Stephen J Kiniry, Gary Loughran, Audrey M. Michel, Дмитрий Рачинский, Pavel V. Baranov
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj-cs.299

A survey of accepted authors in computer systems conferences
Cited by: 4
Author(s): Eitan Frachtenberg, Noah Koster
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-15-S14-S5

EXACT2: the semantics of biomedical protocols
Cited by: 22
Author(s): Larisa Soldatova, Daniel Nadis, Ross D. King, Piyali S. Basu, E. Haddi, Véronique Baumlé, N. Saunders, Wolfgang Marwan, Brian B. Rudkin
Software Mentions: 1
Published: over 9 years ago

10.1002/ece3.6147

Three critical factors affecting automated image species recognition performance for camera traps
Cited by: 69
Author(s): Stefan Schneider, Saul Greenberg, Graham W. Taylor, Stefan C. Kremer
Software Mentions: 1
Published: about 4 years ago

Projects: pypi: github

Papers Mentioning github 57