cran: rmarkdown | Projects | Ecosyste.ms: Papers

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: over 4 years ago

10.1038/s41598-021-96198-7

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

10.1371/journal.pone.0243927

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

10.1037/rev0000169

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

10.12688/f1000research.20843.1

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

10.1371/journal.pcbi.1006361

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: about 6 years ago

10.3389/fpls.2017.00623

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

10.1186/s13104-019-4179-2

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

10.12688/gatesopenres.12832.2

DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis
Cited by: 7
Author(s): Greg Finak, Bryan T. Mayer, William J. Fulp, Paul Obrecht, Alicia Sato, Eva Yin-han Chung, Drienna Holman, Raphaël Gottardo
Software Mentions: 19
Published: about 6 years ago

10.1186/s12859-019-2879-1

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

10.1038/s41597-019-0171-x

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

10.1128/MRA.00129-19

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

10.3390/genes12071044

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

10.1371/journal.pone.0218310

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

10.1038/s41598-020-76843-3

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

10.1371/journal.pone.0199277

Predictive performance of six mortality risk scores and the development of a novel model in a prospective cohort of patients undergoing valve surgery secondary to rheumatic fever
Cited by: 13
Author(s): Omar Asdrúbal Vilca Mejía, Manuel J. Antunes, Maxim Goncharov, Luís Alberto Oliveira Dallan, Elinthon Tavares Veronese, Gisele Aparecida Lapenna, Luiz Augusto Ferreira Lisboa, Carlos Manuel de Almeida Brandão, Jorge P. Zubelli, Flávio Tarasoutchi, Pablo Maria Alberto Pomerantzeff, Fábio Biscegli Jatene
Software Mentions: 13
Published: about 6 years ago

10.1038/s41398-021-01596-0

Autoantibody profiles associated with clinical features in psychotic disorders
Cited by: 6
Author(s): August Jernbom Falk, Cherrie Galletly, David R. Just, Catherine Toben, Bernhard T. Baune, Scott Clark, Dennis Liu, Peter Nilsson, Anna Månberg, Klaus Oliver Schubert
Software Mentions: 13
Published: about 3 years ago

10.1099/mgen.0.000583

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

10.12688/f1000research.6379.2

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

10.1371/journal.pone.0243295

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

10.3389/fmolb.2021.635074

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

10.1093/gbe/evab028

sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R
Cited by: 14
Author(s): Kuan-Hao Chao, Kirston Barton, Sarah Palmer, Robert Lanfear
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pgen.1008126

Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content
Cited by: 14
Author(s): Marco Giovannetti, Christian Göschl, Christof Dietzen, Stig Uggerhøj Andersen, Stanislav Kopriva, Wolfgang Busch
Software Mentions: 10
Published: almost 5 years ago

10.1371/journal.pone.0244122

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

10.1371/journal.pone.0233309

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

10.1371/journal.pone.0198311

GCalignR: An R package for aligning gas-chromatography data for ecological and evolutionary studies
Cited by: 35
Author(s): Meinolf Ottensmann, Martin Stoffel, Hazel J. Nichols, Joseph I. Hoffman
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-019-42713-w

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

10.3389/fonc.2019.01569

The Impact of Surgery in IDH 1 Wild Type Glioblastoma in Relation With the MGMT Deregulation
Cited by: 13
Author(s): Francesco Marchi, Nora Sahnane, Roberta Cerutti, Debora Cipriani, Jessica Barizzi, Federico Mattia Stefanini, Samantha Epistolio, Michele Cerati, Sergio Balbi, Luca Mazzucchelli, Fausto Sessa, G. Pesce, Michael Reinert, Milo Frattini
Software Mentions: 6
Published: over 4 years ago

10.5334/joc.161

The Trajectory of Truth: A Longitudinal Study of the Illusory Truth Effect
Cited by: 14
Author(s): Emma Henderson, Daniel J. Simons, Dale J. Barr
Software Mentions: 5
Published: almost 4 years ago

10.3390/ijerph17155451

A Meta-Analysis of Stressors from the Total Environment Associated with Children’s General Cognitive Ability
Cited by: 16
Author(s): Frances M. Nilsen, Jazmin Del Carmen Ruiz, Nicolle S. Tulve
Software Mentions: 4
Published: about 4 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: over 6 years ago

10.1371/journal.pone.0212390

Facilitating reproducible project management and manuscript development in team science: The projects R package
Cited by: 3
Author(s): Nikolas I. Krieger, Adam T. Perzynski, Jarrod E. Dalton
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2020.518991

A Stomatal Model of Anatomical Tradeoffs Between Gas Exchange and Pathogen Colonization
Cited by: 4
Author(s): Christopher D. Muir
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0255515

Trade informativeness and liquidity in Bitcoin markets
Cited by: 2
Author(s): J. Christopher Westland
Software Mentions: 3
Published: about 3 years ago

10.6061/clinics/2019/e1070

Steatosis and steatohepatitis found in adults after death due to non-burn trauma
Cited by: 2
Author(s): Paulo Reis-Júnior, Ryan Tanigawa, Gustavo Heluani Antunes de Mesquita, Natália Pinheiro Basan, Venâncio Avancini Ferreira Alves, Luiz Augusto Carneiro D’Albuquerque, Wellington Andraus
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.11757

Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey
Cited by: 7
Author(s): Babett Günther, Jean‐Marc Fromentin, Luisa Métral, Sophie Arnaud‐Haond
Software Mentions: 2
Published: about 3 years ago

10.1186/s13104-017-2824-1

Low toxicity and favorable clinical and quality of life impact after non-myeloablative autologous hematopoietic stem cell transplant in Crohn’s disease
Cited by: 18
Author(s): Milton Artur Ruiz, Roberto Luiz Kaiser, Luiz Gustavo de Quadros, Lílian Piron-Ruiz, Tatiana Peña-Arciniegas, Mikaell Alexandre Gouvêa Faria, Rubens Camargo Siqueira, Flavio Fontes Pirozzi, Fernanda Soubhia Liedtke Kaiser, Richard K. Burt
Software Mentions: 2
Published: almost 7 years ago

10.1186/s40359-021-00534-5

Predictive factors of quality of life among medical students: results from a multicentric study
Cited by: 14
Author(s): Antonia Celene Miguel, Patrícia Zen Tempski, Renata Kobayasi, Fernanda Brenneisen Mayer, Mílton A. Martins
Software Mentions: 2
Published: over 3 years ago

Projects: cran: rmarkdown

Papers Mentioning rmarkdown 38