cran: devtools | Projects | Ecosyste.ms: Papers

10.1186/1471-2156-15-81

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: over 10 years ago

10.12688/f1000research.9973.2

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Cited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: almost 6 years ago

10.1186/s12859-017-1905-4

ADAGE signature analysis: differential expression analysis with data-defined gene sets
Cited by: 15
Author(s): Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Software Mentions: 25
Published: over 6 years ago

10.1016/j.xpro.2020.100085

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: almost 4 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 Québec
Cited 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: over 3 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: over 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 Cancer
Cited by: 32
Author(s): Derek J. Essegian, Rimpi Khurana, Vasileios Stathias, Stephan C. Schürer
Software Mentions: 21
Published: almost 4 years ago

10.1038/s41421-020-00226-1

Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo
Cited by: 68
Author(s): Hang‐Ping Yao, Xiangyun Lu, Qiong Chen, Kaijin Xu, Yu Chen, Ming-Hui Cheng, Keda Chen, Linfang Cheng, Tian-Hao Weng, Danrong Shi, Fumin Liu, Zhigang Wu, Mingjie Xie, Haibo Wu, Changzhong Jin, Min Zheng, Nanping Wu, Chao Jiang, Lanjuan Li
Software Mentions: 21
Published: over 3 years ago

10.7717/peerj.5794

beadplexr: reproducible and automated analysis of multiplex bead assays
Cited by: 4
Author(s): Ulrik Stervbo, Timm H. Westhoff, Nina Babel
Software Mentions: 20
Published: over 5 years ago

10.1155/2020/5418364

A Nomogram Based on Radiomics with Mammography Texture Analysis for the Prognostic Prediction in Patients with Triple-Negative Breast Cancer
Cited by: 9
Author(s): Xian Jiang, Xiuhe Zou, Jing Sun, Aiping Zheng, Chao Su
Software Mentions: 20
Published: almost 4 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: almost 6 years ago

10.1093/molbev/msaa311

A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance
Cited by: 15
Author(s): Camille Ameline, Yann Bourgeois, Felix Vögtli, Eevi Savola, Jason P. Andras, Jan Engelstädter, Dieter Ebert
Software Mentions: 19
Published: over 3 years ago

10.1371/journal.pntd.0005121

Seasonal and Spatial Environmental Influence on Opisthorchis viverrini Intermediate Hosts, Abundance, and Distribution: Insights on Transmission Dynamics and Sustainable Control
Cited by: 20
Author(s): Christina Sunyoung Kim, Pierre Echaubard, Apiporn Suwannatrai, Sasithorn Kaewkes, Bruce A. Wilcox, Banchob Sripa
Software Mentions: 19
Published: over 7 years ago

10.1186/s12864-021-07370-2

GCSscore: an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarrays
Cited by: 3
Author(s): Guy M. Harris, Shahroze Abbas, Michael F. Miles
Software Mentions: 17
Published: over 3 years ago

10.1534/g3.119.400018

BGData - A Suite of R Packages for Genomic Analysis with Big Data
Cited by: 23
Author(s): Alexander Grueneberg, Gustavo de los Campos
Software Mentions: 16
Published: about 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: about 5 years ago

10.1016/j.xpro.2021.100768

A computational approach for identification of core modules from a co-expression network and GWAS data
Cited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: almost 3 years ago

10.3389/fpsyg.2021.727737

Psychological Balance Scale: Validation Studies of an Integrative Measure of Well-Being
Cited by: 7
Author(s): Anastasia Besika, Andrea B. Horn, Mike Martin
Software Mentions: 16
Published: almost 3 years ago

10.12688/f1000research.27268.1

rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
Cited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: over 3 years ago

10.12688/f1000research.22139.2

scRepertoire: An R-based toolkit for single-cell immune receptor analysis
Cited by: 121
Author(s): Nicholas Borcherding, Nicholas L. Bormann, Gloria Kraus
Software Mentions: 16
Published: about 4 years ago

10.1038/s41598-017-11514-4

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles
Cited by: 121
Author(s): Lindsay A. Parnell, Catherine Briggs, Bin Cao, Omar Delannoy-Bruno, Andrew E. Schrieffer, Indira U. Mysorekar
Software Mentions: 16
Published: almost 7 years ago

10.1038/s41598-021-81688-5

Fungal diversity and community structure from coastal and barrier island beaches in the United States Gulf of Mexico
Cited by: 14
Author(s): Allison K. Walker, Brent M. Robicheau
Software Mentions: 16
Published: over 3 years ago

10.1128/mBio.02120-17

Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients
Cited by: 95
Author(s): Matthew K. Doherty, Tao Ding, Charlie C. Koumpouras, Shannon Telesco, Calixte S. Monast, Anuk Das, Carrie Brodmerkel, Patrick D. Schloss
Software Mentions: 15
Published: about 6 years ago

10.1371/journal.pone.0091650

rAvis: An R-Package for Downloading Information Stored in Proyecto AVIS, a Citizen Science Bird Project
Cited by: 6
Author(s): Sara Varela, Javier González-Hernández, Eduardo Casabella, Rafael Barrientos
Software Mentions: 15
Published: over 10 years ago

10.1002/ece3.3240

feedrand animalnexus.ca: A paired R package and user-friendly Web application for transforming and visualizing animal movement data from static stations
Cited by: 9
Author(s): Steffi LaZerte, Matthew W. Reudink, Ken A. Otter, Jackson W. Kusack, Jacob Bailey, A. Woolverton, Mark Paetkau, Adriaan de Jong, David Hill
Software Mentions: 14
Published: almost 7 years ago

10.1186/s13073-021-00907-w

Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses
Cited by: 5
Author(s): Rosanne C. van Deuren, Peer Arts, Giulio Cavalli, Martin Jaeger, Marloes Steehouwer, Maartje van de Vorst, Christian Gilissen, Leo A. B. Joosten, Charles A. Dinarello, Musa M. Mhlanga, Vinod Kumar, Mihai G. Netea, Frank L. van de Veerdonk, Alexander Hoischen
Software Mentions: 14
Published: about 3 years ago

10.1371/journal.pone.0223542

Joint emulation of Earth System Model temperature-precipitation realizations with internal variability and space-time and cross-variable correlation: fldgen v2.0 software description
Cited by: 3
Author(s): Abigail Snyder, Robert Link, Kalyn Dorheim, Ben Kravitz, Ben Bond‐Lamberty, Corinne Hartin
Software Mentions: 14
Published: almost 5 years ago

10.12688/f1000research.12512.1

lakemorpho: Calculating lake morphometry metrics in R
Cited by: 15
Author(s): Jeffrey W. Hollister, Joseph Stachelek
Software Mentions: 13
Published: almost 7 years ago

10.1186/s13227-020-0147-0

Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean, Thamnocephalus platyurus
Cited by: 9
Author(s): Savvas J. Constantinou, Nicole Duan, Lisa M. Nagy, Ariel D. Chipman, Terri A. Williams
Software Mentions: 13
Published: over 4 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

10.3389/fmicb.2019.00665

Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front
Cited by: 31
Author(s): Gilda Varliero, Christina Bienhold, Florian Schmid, Antje Boetius, Massimiliano Molari
Software Mentions: 13
Published: about 5 years ago

10.1534/g3.120.401527

rdmc: An Open Source R Package Implementing Convergent Adaptation Models of Lee and Coop (2017)
Cited by: 2
Author(s): Silas Tittes
Software Mentions: 12
Published: almost 4 years ago

10.1186/s40168-020-0793-4

Separating the signal from the noise in metagenomic cell-free DNA sequencing
Cited by: 26
Author(s): Philip Burnham, Nardhy Gómez-López, Michael Heyang, Alexandre Pellan Cheng, Joan Sesing Lenz, Darshana Dadhania, John Richard Lee, Manikkam Suthanthiran, Roberto Romero, Iwijn De Vlaminck
Software Mentions: 12
Published: over 4 years ago

10.1162/CPSY_a_00002

Revealing Neurocomputational Mechanisms of Reinforcement Learning and Decision-Making With the hBayesDM Package
Cited by: 204
Author(s): Woo-Young Ahn, Nathaniel Haines, Lei Zhang
Software Mentions: 12
Published: almost 7 years ago

10.1038/s41598-021-85155-z

Validating machine learning approaches for prediction of donor related complication in microsurgical breast reconstruction: a retrospective cohort study
Cited by: 6
Author(s): Yujin Myung, Sungmi Jeon, Chan Yeong Heo, Eun‐Kyu Kim, Eunyoung Kang, Hee-Chul Shin, Eun Joo Yang, Jae Hoon Jeong
Software Mentions: 12
Published: over 3 years ago

10.12688/f1000research.14013.2

Taxa: An R package implementing data standards and methods for taxonomic data
Cited by: 23
Author(s): Zachary Foster, Scott Chamberlain, Niklaus J. Grünwald
Software Mentions: 12
Published: almost 6 years ago

10.3389/fnbeh.2018.00187

Exhaustive Multi-Parametric Assessment of the Behavioral Array of Daily Activities of Mice Using Cluster and Factor Analysis
Cited by: 7
Author(s): Kenzo Yamamoto, Katsiaryna V. Gris, Jesús E. Sotelo Fonseca, Marjan Gharagozloo, Shaimaa Mahmoud, Camille Simard, Daphné Houle-Martel, Theodore Cloutier, Pavel Gris, Denis Gris
Software Mentions: 12
Published: almost 6 years ago

10.1186/1476-069X-13-57

The identification of complex interactions in epidemiology and toxicology: a simulation study of boosted regression trees
Cited by: 45
Author(s): Erik Lampa, Lars Lind, P. Monica Lind, Anna Bornefalk-Hermansson
Software Mentions: 11
Published: about 10 years ago

10.12688/f1000research.26771.2

HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas
Cited by: 1
Author(s): Tim O. Nieuwenhuis, Marc K. Halushka
Software Mentions: 11
Published: over 3 years ago

10.1186/s12866-020-02075-0

Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments
Cited by: 11
Author(s): Zala Schmautz, Carlos Espinal, Andrea M. Bohny, Fabio Rezzonico, Ranka Junge, Emmanuel Frossard, Theo H. M. Smits
Software Mentions: 11
Published: over 3 years ago

10.3897/BDJ.6.e20760

spind: an R Package to Account for Spatial Autocorrelation in the Analysis of Lattice Data
Cited by: 7
Author(s): Gudrun Carl, Sam Levin, Ingolf Kühn
Software Mentions: 11
Published: over 6 years ago

10.3897/BDJ.9.e71378

Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank
Cited by: 2
Author(s): Reginald H.F. Young, Rekkab Gill, Daniel Gillis, Robert Hanner
Software Mentions: 11
Published: almost 3 years ago

10.7717/peerj.10680

Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinoma
Cited by: 5
Author(s): Shaoyong Zheng, Lan Yao, Fasheng Li, Luyu Huang, Yunfang Yu, Zenan Lin, Hao Li, Xiance Jin, Michael Lanuti, Haiyu Zhou
Software Mentions: 11
Published: over 3 years ago

10.1534/g3.120.401270

Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans’ Gene Expression Data
Cited by: 7
Author(s): Michael Cary, Katie Podshivalova, Cynthia Kenyon
Software Mentions: 11
Published: almost 4 years ago

10.3390/ijerph17197153

Association between Maternal Postpartum Depression, Stress, Optimism, and Breastfeeding Pattern in the First Six Months
Cited by: 33
Author(s): Andrea Gila-Díaz, Gloria Herranz Carrillo, Ángel L. López de Pablo, Silvia M. Arribas, David Ramiro-Cortijo
Software Mentions: 11
Published: almost 4 years ago

10.1002/ece3.4550

Size does matter: Parallel evolution of adaptive thermal tolerance and body size facilitates adaptation to climate change in domestic cattle
Cited by: 20
Author(s): Muhammed Elayadeth-Meethal, Aravindakshan Thazhathu Veettil, Shane K. Maloney, N. J. Hawkins, Tom Misselbrook, Veerasamy Sejian, M. Jordana Rivero, Michael R. F. Lee
Software Mentions: 10
Published: almost 6 years ago

10.1186/s12957-021-02162-0

The preoperative prognostic value of the radiomics nomogram based on CT combined with machine learning in patients with intrahepatic cholangiocarcinoma
Cited by: 16
Author(s): Youyin Tang, Tao Zhang, Xianghong Zhou, Ying Zhao, Hanyue Xu, Yichun Liu, Hang Wang, Zheyu Chen, Xuelei Ma
Software Mentions: 10
Published: almost 3 years ago

10.1093/bib/bbv108

Dimension reduction techniques for the integrative analysis of multi-omics data
Cited 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

10.7150/ijms.53602

Development and validation of a comprehensive radiomics nomogram for prognostic prediction of primary hepatic sarcomatoid carcinoma after surgical resection
Cited by: 5
Author(s): Youyin Tang, Tao Zhang, Ying Zhao, Zhe-Yu Chen, Xuelei Ma
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0185171

Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes
Cited by: 29
Author(s): Tuulia Mali, Jaana Kuuskeri, Firoz Shah, Taina Lundell
Software Mentions: 10
Published: almost 7 years ago

10.1371/journal.pbio.3001053

Identification of 3′ UTR motifs required for mRNA localization to myelin sheaths in vivo
Cited by: 13
Author(s): Katie M. Yergert, Caleb A. Doll, Rebecca O’Rouke, Jacob H. Hines, Bruce Appel
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.8027

Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps
Cited by: 0
Author(s): Cédric Boué, Tonia DeBellis, Lisa Venier, Timothy T. Work, Steven W. Kembel
Software Mentions: 10
Published: over 4 years ago

10.3389/fgene.2020.00260

IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix
Cited by: 20
Author(s): Fengyu He, Shuangcheng Ding, Hongwei Wang, Feng Qin
Software Mentions: 10
Published: over 4 years ago

10.1002/ece3.5412

learnPopGen : An R package for population genetic simulation and numerical analysis
Cited by: 6
Author(s): Liam J. Revell
Software Mentions: 10
Published: about 5 years ago

10.1186/s12939-018-0750-z

Detecting spatio-temporal mortality clusters of European countries by sex and age
Cited by: 9
Author(s): Patricia Carracedo, Ana Debón, Adina Iftimi, Francisco Montes
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0157423

Decline of a Rare Moth at Its Last Known English Site: Causes and Lessons for Conservation
Cited by: 2
Author(s): D. James Baker, Sinead Barrett, Colin M. Beale, Terry J. Crawford, Sam Ellis, Tallulah Gullett, Peter J. Mayhew, Mark Parsons, Penny Relf, Paul B. Robertson, J. L. Small, David Wainwright
Software Mentions: 9
Published: about 8 years ago

10.3390/md18120649

Sustainable Low-Volume Analysis of Environmental Samples by Semi-Automated Prioritization of Extracts for Natural Product Research (SeaPEPR)
Cited by: 6
Author(s): Riyanti, Michael Marner, Christoph Hartwig, Maria A. Patras, Stevy Imelda Murniati Wodi, Frets Jonas Rieuwpassa, Frans Gruber Ijong, Walter Balansa, Till F. Schäberle
Software Mentions: 9
Published: over 3 years ago

10.1186/s12859-020-03910-x

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
Cited by: 48
Author(s): Sebastian Canzler, Jörg Hackermüller
Software Mentions: 9
Published: over 3 years ago

10.3389/fpsyg.2019.01507

A Primer to (Cross-Cultural) Multi-Group Invariance Testing Possibilities in R
Cited by: 147
Author(s): Ronald Fischer, Johannes Alfons Karl
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12885-019-6235-7

lionessR: single sample network inference in R
Cited by: 22
Author(s): Marieke L. Kuijjer, Ping-Han Hsieh, John Quackenbush, Kimberly Glass
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0228198

iCARE: An R package to build, validate and apply absolute risk models
Cited by: 56
Author(s): Parichoy Pal Choudhury, Paige Maas, Amber N. Wilcox, William Wheeler, Mark N. Brook, David P. Check, Montserrat García-Closas, Nilanjan Chatterjee
Software Mentions: 8
Published: over 4 years ago

10.1016/j.epidem.2020.100425

Responsible modelling: Unit testing for infectious disease epidemiology
Cited by: 6
Author(s): Tim Lucas, Timothy M. Pollington, Emma L Davis, T. Déirdre Hollingsworth
Software Mentions: 8
Published: over 3 years ago

10.7717/peerj.2436

RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistry
Cited by: 65
Author(s): Jing Zhang, Kenneth B. Storey
Software Mentions: 8
Published: almost 8 years ago

10.1038/s41598-020-59062-8

Sting nematodes modify metabolomic profiles of host plants
Cited by: 4
Author(s): Denis S. Willett, Camila C. Filgueiras, Nicole Benda, Jing Zhang, Kevin E. Kenworthy
Software Mentions: 8
Published: over 4 years ago

10.15252/msb.20188238

Unraveling mitotic protein networks by 3D multiplexed epitope drug screening
Cited by: 1
Author(s): Lorenz Maier, Stefan M. Kallenberger, Katharina Jechow, Marcel Waschow, Roland Eils, Christian Conrad
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-020-76256-2

Selection of sponge-associated bacteria with high potential for the production of antibacterial compounds
Cited by: 11
Author(s): Riyanti, Walter Balansa, Yang Liu, Abha Sharma, Sanja Mihajlović, Christoph Hartwig, Benedikt Leis, Frets Jonas Rieuwpassa, Frans Gruber Ijong, Heike Wägele, Gabriele M. König, Till F. Schäberle
Software Mentions: 8
Published: over 3 years ago

10.3390/biology10040314

Connectivity of Edaphic and Endolithic Microbial Niches in Cold Mountain Desert of Eastern Pamir (Tajikistan)
Cited by: 6
Author(s): Nataliia Khomutovska, Asunción de los Rı́os, Marcin Syczewski, Iwona Jasser
Software Mentions: 8
Published: about 3 years ago

10.3390/nu13072372

Assessment of Adherence to the Healthy Food Pyramid in Pregnant and Lactating Women
Cited by: 5
Author(s): Andrea Gila-Díaz, Ariadna Witte Castro, Gloria Herranz Carrillo, Pratibha Singh, William Yakah, Silvia M. Arribas, David Ramiro-Cortijo
Software Mentions: 8
Published: almost 3 years ago

10.1534/g3.119.400126

An R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction
Cited by: 38
Author(s): Osval A. Montesinos-L֯ópez, Abelardo Montesinos‐López, Francisco Javier Luna-Vázquez, Fernando H. Toledo, Paulino Pérez‐Rodríguez, Morten Lillemo, J. Crossa
Software Mentions: 8
Published: about 5 years ago

10.7717/peerj.11865

ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences
Cited by: 2
Author(s): Dylan Catlett, Kevin Son, Connie Liang
Software Mentions: 7
Published: almost 3 years ago

10.3390/nu12092569

Influence of Maternal Age and Gestational Age on Breast Milk Antioxidants During the First Month of Lactation
Cited by: 17
Author(s): Andrea Gila-Díaz, Gloria Herranz Carrillo, Silvia Cañas, Miguel Sáenz de Pipaón, José Martínez‐Orgado, Pilar Rodríguez-Rodríguez, Ángel L. López de Pablo, María Á. Martín-Cabrejas, David Ramiro-Cortijo, Silvia M. Arribas
Software Mentions: 7
Published: almost 4 years ago

10.1186/s40851-019-0136-0

A new calmanostracan crustacean species from the Cretaceous Yixian Formation and a simple approach for differentiating fossil tadpole shrimps and their relatives
Cited by: 3
Author(s): Philipp Wagner, Joachim T. Haug, Carolin Haug
Software Mentions: 7
Published: about 5 years ago

10.1186/s13321-015-0086-2

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules
Cited by: 36
Author(s): Daniel S. Murrell, Isidro Cortés-Ciriano, Gerard J. P. van Westen, Ian P. Stott, Andreas Bender, Thérèse E. Malliavin, Robert C. Glen
Software Mentions: 7
Published: almost 9 years ago

10.3389/fgene.2015.00287

Design, measurement and processing of region-specific DNA methylation assays: the mass spectrometry-based method EpiTYPER
Cited by: 56
Author(s): H. Eka D. Suchiman, Roderick C. Slieker, Dennis Kremer, P. Eline Slagboom, Bastiaan T. Heijmans, Elmar W. Tobi
Software Mentions: 7
Published: almost 9 years ago

10.1371/journal.pone.0171784

rEHR: An R package for manipulating and analysing Electronic Health Record data
Cited by: 14
Author(s): David A. Springate, Rosa Parisi, Iván Olier, David Reeves, Evangelos Kontopantelis
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0229763

Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform
Cited by: 8
Author(s): Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0254293

easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application
Cited by: 4
Author(s): Matteo Di Bernardo, Timothy A. Crombie, Daniel E. Cook, Erik C. Andersen
Software Mentions: 7
Published: over 2 years ago

10.7554/eLife.14334

TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics
Cited by: 104
Author(s): Raphaël Etournay, Matthias Merkel, Marko Popović, Holger Brandl, Natalie A. Dye, Benoît Aigouy, Guillaume Salbreux, Suzanne Eaton, Frank Jülicher
Software Mentions: 7
Published: about 8 years ago

10.3897/BDJ.6.e23635

The taxlist package: managing plant taxonomic lists in R
Cited by: 5
Author(s): Miguel Álvarez, Federico Luebert
Software Mentions: 7
Published: about 6 years ago

10.1002/cpz1.60

Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo
Cited by: 24
Author(s): Xavier Didelot, Michaela Kendall, Yuanwei Xu, Peter J White, Noel D. McCarthy
Software Mentions: 7
Published: over 3 years ago

10.3897/BDJ.7.e31511

rMyCoPortal - an R package to interface with the Mycology Collections Portal
Cited by: 3
Author(s): Franz‐Sebastian Krah, Scott T. Bates, Andrew N. Miller
Software Mentions: 6
Published: over 5 years ago

10.3390/cancers13102496

Differential Prognosis and Response of Denovo vs. Secondary Muscle-Invasive Bladder Cancer: An Updated Systematic Review and Meta-Analysis
Cited by: 8
Author(s): Matthias Pones, David D’Andrea, Keiichiro Mori, Mohammad Abufraj, Marco Moschini, Éva Compérat, Shahrokh F. Shariat
Software Mentions: 6
Published: about 3 years ago

10.3758/s13428-020-01436-x

Sharing and organizing research products as R packages
Cited by: 6
Author(s): Matti Vuorre, Matthew J. C. Crump
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0237272

Passenger-surface microbiome interactions in the subway of Mexico City
Cited by: 10
Author(s): Daniela Vargas-Robles, Carolina Gonzalez-Cedillo, Apolinar M. Hernández, Luis David Alcaraz, Mariana Peimbert
Software Mentions: 6
Published: almost 4 years ago

10.1007/s00604-018-3195-6

A smartphone readout system for gold nanoparticle-based lateral flow assays: application to monitoring of digoxigenin
Cited by: 46
Author(s): Christoph Ruppert, Navneet Phogat, Stefan Laufer, Matthias Kohl, Hans‐Peter Deigner
Software Mentions: 6
Published: over 5 years ago

10.1186/s12882-020-01773-1

The urinary microbiome shows different bacterial genera in renal transplant recipients and non-transplant patients at time of acute kidney injury – a pilot study
Cited by: 10
Author(s): Daniela Gerges, Peter Pichler, Alexander Zimprich, Christoph Hotzy, Wolfgang Barousch, Rita Lang, Elisabeth Lobmeyr, Sabina Baumgartner‐Parzer, Ludwig Wagner, Wolfgang Winnicki
Software Mentions: 6
Published: over 4 years ago

10.1186/s12866-019-1672-7

An improved bind-n-seq strategy to determine protein-DNA interactions validated using the bacterial transcriptional regulator YipR
Cited by: 26
Author(s): Shi-Qi An, Miguel A. Valvano, Yu Yi, Jeremy S. Webb, Guillermo López–Campos
Software Mentions: 6
Published: over 4 years ago

10.1093/g3journal/jkab040

EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture
Cited by: 44
Author(s): Germano Costa‐Neto, Giovanni Galli, Humberto Fanelli Carvalho, J. Crossa, Roberto Fritsche‐Neto
Software Mentions: 6
Published: over 3 years ago

10.1186/s12859-019-2780-y

Focused multidimensional scaling: interactive visualization for exploration of high-dimensional data
Cited by: 11
Author(s): Lea Urpa, Simon Anders
Software Mentions: 6
Published: about 5 years ago

10.2174/1874104501711010212

Ezqsar: An R Package for Developing QSAR Models Directly From Structures
Cited by: 10
Author(s): Jamal Shamsara
Software Mentions: 6
Published: over 6 years ago

10.1111/1755-0998.12676

<scp>treespace</scp> : Statistical exploration of landscapes of phylogenetic trees
Cited by: 131
Author(s): Thibaut Jombart, Michaela Kendall, Jacob Almagro-Garcia, Caroline Colijn
Software Mentions: 6
Published: about 7 years ago

10.7717/peerj-cs.520

dxpr: an R package for generating analysis-ready data from electronic health records—diagnoses and procedures
Cited by: 2
Author(s): Yi-Ju Tseng, Hsiang Ju Chiu, Chun Ju Chen
Software Mentions: 6
Published: about 3 years ago

10.3389/fpls.2019.01184

Ramf: An Open-Source R Package for Statistical Analysis and Display of Quantitative Root Colonization by Arbuscular Mycorrhiza Fungi
Cited by: 2
Author(s): Marco Chiapello, Debatosh Das, Caroline Gutjahr
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-017-06880-y

A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis
Cited by: 29
Author(s): Fiona Fouhy, N.J. Ronan, Órla O’Sullivan, Yvonne McCarthy, Aaron M. Walsh, Desmond M. Murphy, Mary B. Daly, Evelyn Flanagan, C. Fleming, M. McCarthy, C. Shortt, Joseph A. Eustace, Fergus Shanahan, Mary C. Rea, R. Paul Ross, Catherine Stanton, Barry J. Plant
Software Mentions: 6
Published: almost 7 years ago

10.7717/peerj.4402

Comparative genomic analysis of a new tellurite-resistantPsychrobacterstrain isolated from the Antarctic Peninsula
Cited by: 19
Author(s): Claudia Muñoz-Villagrán, Katterinne N. Mendez, Fabián A. Cornejo, Maximiliano Figueroa, Agustina Undabarrena, Eduardo Morales, Mauricio Arenas-Salinas, Felipe Arenas, Eduardo Castro-Nallar, Claudio C. Vásquez
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0228098

How to use frailtypack for validating failure-time surrogate endpoints using individual patient data from meta-analyses of randomized controlled trials
Cited by: 2
Author(s): Casimir Ledoux Sofeu, Virginie Rondeau
Software Mentions: 5
Published: over 4 years ago

10.3390/metabo8010016

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites
Cited by: 27
Author(s): Bofei Zhang, Senyang Hu, Elizabeth Baskin, Andrew Patt, Jalal K. Siddiqui, Ewy A. Mathé
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pcbi.1009182

Sample size calculation for phylogenetic case linkage
Cited by: 7
Author(s): Shirlee Wohl, J. R. Giles, Justin Lessler
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0181109

Hypoxia tolerance and responses to hypoxic stress during heart and skeletal muscle inflammation in Atlantic salmon (Salmo salar)
Cited by: 33
Author(s): Morten Lund, Maria K. Dahle, Gerrit Timmerhaus, Marta Alarcón, Mark D. Powell, Vidar Aspehaug, Espen Rimstad, Sven Martin Jørgensen
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0121760

medplot: A Web Application for Dynamic Summary and Analysis of Longitudinal Medical Data Based on R
Cited by: 5
Author(s): Črt Ahlin, Daša Stupica, Franc Strle, Lara Lusa
Software Mentions: 5
Published: over 9 years ago

Projects: cran: devtools

Papers Mentioning devtools 157