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: pypi: devtools
https://packages.ecosyste.ms/registries/pypi.org/packages/devtools
Python's missing debug print command, and more.
18 versions
Latest release: about 1 year ago
43 dependent packages
244,858 downloads last month
Papers Mentioning devtools 157
10.1186/1471-2156-15-81
Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrationsCited 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: almost 11 years ago
10.12688/f1000research.9973.2
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment testsCited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: over 6 years ago
10.1186/s12859-017-1905-4
ADAGE signature analysis: differential expression analysis with data-defined gene setsCited by: 15
Author(s): Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Software Mentions: 25
Published: almost 7 years ago
10.1016/j.xpro.2020.100085
Protocol for Identification and Removal of Doublets with DoubletDeconCited by: 7
Author(s): Erica A. K. DePasquale, Daniel Schnell, Kashish Chetal, Nathan Salomonis
Software Mentions: 25
Published: about 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 QuébecCited 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: almost 4 years ago
10.12688/f1000research.20843.1
Creating and sharing reproducible research code the workflowr wayCited by: 51
Author(s): John Blischak, Peter Carbonetto, Matthew Stephens
Software Mentions: 22
Published: about 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 CancerCited by: 32
Author(s): Derek J. Essegian, Rimpi Khurana, Vasileios Stathias, Stephan C. Schürer
Software Mentions: 21
Published: about 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 vivoCited 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: about 4 years ago
10.7717/peerj.5794
beadplexr: reproducible and automated analysis of multiplex bead assaysCited by: 4
Author(s): Ulrik Stervbo, Timm H. Westhoff, Nina Babel
Software Mentions: 20
Published: about 6 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 CancerCited by: 9
Author(s): Xian Jiang, Xiuhe Zou, Jing Sun, Aiping Zheng, Chao Su
Software Mentions: 20
Published: about 4 years ago
10.12688/gatesopenres.12832.2
DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysisCited 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: over 6 years ago
10.1093/molbev/msaa311
A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host ResistanceCited by: 15
Author(s): Camille Ameline, Yann Bourgeois, Felix Vögtli, Eevi Savola, Jason P. Andras, Jan Engelstädter, Dieter Ebert
Software Mentions: 19
Published: almost 4 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 ControlCited by: 20
Author(s): Christina Sunyoung Kim, Pierre Echaubard, Apiporn Suwannatrai, Sasithorn Kaewkes, Bruce A. Wilcox, Banchob Sripa
Software Mentions: 19
Published: almost 8 years ago
10.1186/s12864-021-07370-2
GCSscore: an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarraysCited by: 3
Author(s): Guy M. Harris, Shahroze Abbas, Michael F. Miles
Software Mentions: 17
Published: almost 4 years ago
10.1534/g3.119.400018
BGData - A Suite of R Packages for Genomic Analysis with Big DataCited by: 23
Author(s): Alexander Grueneberg, Gustavo de los Campos
Software Mentions: 16
Published: over 5 years ago
10.1128/MRA.00129-19
omu, a Metabolomics Count Data Analysis Tool for Intuitive Figures and Convenient Metadata CollectionCited by: 12
Author(s): Connor R. Tiffany, Andreas J. Bäumler
Software Mentions: 16
Published: over 5 years ago
10.1016/j.xpro.2021.100768
A computational approach for identification of core modules from a co-expression network and GWAS dataCited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: about 3 years ago
10.3389/fpsyg.2021.727737
Psychological Balance Scale: Validation Studies of an Integrative Measure of Well-BeingCited by: 7
Author(s): Anastasia Besika, Andrea B. Horn, Mike Martin
Software Mentions: 16
Published: about 3 years ago
10.12688/f1000research.27268.1
rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsisCited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: almost 4 years ago
10.12688/f1000research.22139.2
scRepertoire: An R-based toolkit for single-cell immune receptor analysisCited by: 121
Author(s): Nicholas Borcherding, Nicholas L. Bormann, Gloria Kraus
Software Mentions: 16
Published: over 4 years ago
10.1038/s41598-017-11514-4
Microbial communities in placentas from term normal pregnancy exhibit spatially variable profilesCited by: 121
Author(s): Lindsay A. Parnell, Catherine Briggs, Bin Cao, Omar Delannoy-Bruno, Andrew E. Schrieffer, Indira U. Mysorekar
Software Mentions: 16
Published: about 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 MexicoCited by: 14
Author(s): Allison K. Walker, Brent M. Robicheau
Software Mentions: 16
Published: almost 4 years ago
10.1128/mBio.02120-17
Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease PatientsCited 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: over 6 years ago
10.1371/journal.pone.0091650
rAvis: An R-Package for Downloading Information Stored in Proyecto AVIS, a Citizen Science Bird ProjectCited 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 stationsCited 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: about 7 years ago
10.1186/s13073-021-00907-w
Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responsesCited 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: over 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 descriptionCited by: 3
Author(s): Abigail Snyder, Robert Link, Kalyn Dorheim, Ben Kravitz, Ben Bond‐Lamberty, Corinne Hartin
Software Mentions: 14
Published: about 5 years ago
10.12688/f1000research.12512.1
lakemorpho: Calculating lake morphometry metrics in RCited by: 15
Author(s): Jeffrey W. Hollister, Joseph Stachelek
Software Mentions: 13
Published: about 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 platyurusCited by: 9
Author(s): Savvas J. Constantinou, Nicole Duan, Lisa M. Nagy, Ariel D. Chipman, Terri A. Williams
Software Mentions: 13
Published: almost 5 years ago
10.12688/f1000research.7082.3
EvolQG - An R package for evolutionary quantitative geneticsCited by: 31
Author(s): Diogo Melo, Guilherme Garcia, Alex Hubbe, Ana Paula A. Assis, Gabriel Marroig
Software Mentions: 13
Published: about 8 years ago
10.3389/fmicb.2019.00665
Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar FrontCited by: 31
Author(s): Gilda Varliero, Christina Bienhold, Florian Schmid, Antje Boetius, Massimiliano Molari
Software Mentions: 13
Published: over 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: about 4 years ago
10.1186/s40168-020-0793-4
Separating the signal from the noise in metagenomic cell-free DNA sequencingCited 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: almost 5 years ago
10.1162/CPSY_a_00002
Revealing Neurocomputational Mechanisms of Reinforcement Learning and Decision-Making With the hBayesDM PackageCited by: 204
Author(s): Woo-Young Ahn, Nathaniel Haines, Lei Zhang
Software Mentions: 12
Published: about 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 studyCited 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 dataCited by: 23
Author(s): Zachary Foster, Scott Chamberlain, Niklaus J. Grünwald
Software Mentions: 12
Published: about 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 AnalysisCited 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: about 6 years ago
10.1186/1476-069X-13-57
The identification of complex interactions in epidemiology and toxicology: a simulation study of boosted regression treesCited by: 45
Author(s): Erik Lampa, Lars Lind, P. Monica Lind, Anna Bornefalk-Hermansson
Software Mentions: 11
Published: over 10 years ago
10.12688/f1000research.26771.2
HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein AtlasCited 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 compartmentsCited 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: almost 4 years ago
10.3897/BDJ.6.e20760
spind: an R Package to Account for Spatial Autocorrelation in the Analysis of Lattice DataCited 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 GenBankCited by: 2
Author(s): Reginald H.F. Young, Rekkab Gill, Daniel Gillis, Robert Hanner
Software Mentions: 11
Published: about 3 years ago
10.7717/peerj.10680
Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinomaCited 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: almost 4 years ago
10.1534/g3.120.401270
Application of Transcriptional Gene Modules to Analysis of <i>Caenorhabditis elegans</i>’ Gene Expression DataCited by: 7
Author(s): Michael Cary, Katie Podshivalova, Cynthia Kenyon
Software Mentions: 11
Published: about 4 years ago
10.3390/ijerph17197153
Association between Maternal Postpartum Depression, Stress, Optimism, and Breastfeeding Pattern in the First Six MonthsCited 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: about 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 cattleCited 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: about 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 cholangiocarcinomaCited 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: over 3 years ago
10.1093/bib/bbv108
Dimension reduction techniques for the integrative analysis of multi-omics dataCited 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 resectionCited by: 5
Author(s): Youyin Tang, Tao Zhang, Ying Zhao, Zhe-Yu Chen, Xuelei Ma
Software Mentions: 10
Published: almost 4 years ago
10.1371/journal.pone.0185171
Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of AgaricomycetesCited by: 29
Author(s): Tuulia Mali, Jaana Kuuskeri, Firoz Shah, Taina Lundell
Software Mentions: 10
Published: about 7 years ago
10.1371/journal.pbio.3001053
Identification of 3′ UTR motifs required for mRNA localization to myelin sheaths in vivoCited by: 13
Author(s): Katie M. Yergert, Caleb A. Doll, Rebecca O’Rouke, Jacob H. Hines, Bruce Appel
Software Mentions: 10
Published: almost 4 years ago
10.7717/peerj.8027
Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumpsCited by: 0
Author(s): Cédric Boué, Tonia DeBellis, Lisa Venier, Timothy T. Work, Steven W. Kembel
Software Mentions: 10
Published: almost 5 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 MatrixCited by: 20
Author(s): Fengyu He, Shuangcheng Ding, Hongwei Wang, Feng Qin
Software Mentions: 10
Published: over 4 years ago
10.1002/ece3.5412
<i>learnPopGen</i> : An R package for population genetic simulation and numerical analysisCited by: 6
Author(s): Liam J. Revell
Software Mentions: 10
Published: over 5 years ago
10.1186/s12939-018-0750-z
Detecting spatio-temporal mortality clusters of European countries by sex and ageCited 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 ConservationCited 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: over 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: almost 4 years ago
10.1186/s12859-020-03910-x
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics dataCited by: 48
Author(s): Sebastian Canzler, Jörg Hackermüller
Software Mentions: 9
Published: almost 4 years ago
10.3389/fpsyg.2019.01507
A Primer to (Cross-Cultural) Multi-Group Invariance Testing Possibilities in RCited by: 147
Author(s): Ronald Fischer, Johannes Alfons Karl
Software Mentions: 9
Published: over 5 years ago
10.1186/s12885-019-6235-7
lionessR: single sample network inference in RCited by: 22
Author(s): Marieke L. Kuijjer, Ping-Han Hsieh, John Quackenbush, Kimberly Glass
Software Mentions: 9
Published: about 5 years ago
10.1371/journal.pone.0228198
iCARE: An R package to build, validate and apply absolute risk modelsCited 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: almost 5 years ago
10.1016/j.epidem.2020.100425
Responsible modelling: Unit testing for infectious disease epidemiologyCited by: 6
Author(s): Tim Lucas, Timothy M. Pollington, Emma L Davis, T. Déirdre Hollingsworth
Software Mentions: 8
Published: almost 4 years ago
10.7717/peerj.2436
RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistryCited by: 65
Author(s): Jing Zhang, Kenneth B. Storey
Software Mentions: 8
Published: about 8 years ago
10.1038/s41598-020-59062-8
Sting nematodes modify metabolomic profiles of host plantsCited by: 4
Author(s): Denis S. Willett, Camila C. Filgueiras, Nicole Benda, Jing Zhang, Kevin E. Kenworthy
Software Mentions: 8
Published: almost 5 years ago
10.15252/msb.20188238
Unraveling mitotic protein networks by 3D multiplexed epitope drug screeningCited by: 1
Author(s): Lorenz Maier, Stefan M. Kallenberger, Katharina Jechow, Marcel Waschow, Roland Eils, Christian Conrad
Software Mentions: 8
Published: over 6 years ago
10.1038/s41598-020-76256-2
Selection of sponge-associated bacteria with high potential for the production of antibacterial compoundsCited 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: about 4 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: over 3 years ago
10.3390/nu13072372
Assessment of Adherence to the Healthy Food Pyramid in Pregnant and Lactating WomenCited 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: over 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 PredictionCited 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: over 5 years ago
10.7717/peerj.11865
ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequencesCited by: 2
Author(s): Dylan Catlett, Kevin Son, Connie Liang
Software Mentions: 7
Published: over 3 years ago
10.3390/nu12092569
Influence of Maternal Age and Gestational Age on Breast Milk Antioxidants During the First Month of LactationCited 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: about 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 relativesCited by: 3
Author(s): Philipp Wagner, Joachim T. Haug, Carolin Haug
Software Mentions: 7
Published: over 5 years ago
10.1186/s13321-015-0086-2
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small moleculesCited 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: about 9 years ago
10.3389/fgene.2015.00287
Design, measurement and processing of region-specific DNA methylation assays: the mass spectrometry-based method EpiTYPERCited 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: about 9 years ago
10.1371/journal.pone.0171784
rEHR: An R package for manipulating and analysing Electronic Health Record dataCited 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 platformCited 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 applicationCited by: 4
Author(s): Matteo Di Bernardo, Timothy A. Crombie, Daniel E. Cook, Erik C. Andersen
Software Mentions: 7
Published: about 3 years ago
10.7554/eLife.14334
TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamicsCited 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: over 8 years ago
10.3897/BDJ.6.e23635
The taxlist package: managing plant taxonomic lists in RCited by: 5
Author(s): Miguel Álvarez, Federico Luebert
Software Mentions: 7
Published: over 6 years ago
10.1002/cpz1.60
Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhyloCited by: 24
Author(s): Xavier Didelot, Michaela Kendall, Yuanwei Xu, Peter J White, Noel D. McCarthy
Software Mentions: 7
Published: almost 4 years ago
10.3897/BDJ.7.e31511
rMyCoPortal - an R package to interface with the Mycology Collections PortalCited by: 3
Author(s): Franz‐Sebastian Krah, Scott T. Bates, Andrew N. Miller
Software Mentions: 6
Published: almost 6 years ago
10.3390/cancers13102496
Differential Prognosis and Response of Denovo vs. Secondary Muscle-Invasive Bladder Cancer: An Updated Systematic Review and Meta-AnalysisCited by: 8
Author(s): Matthias Pones, David D’Andrea, Keiichiro Mori, Mohammad Abufraj, Marco Moschini, Éva Compérat, Shahrokh F. Shariat
Software Mentions: 6
Published: over 3 years ago
10.3758/s13428-020-01436-x
Sharing and organizing research products as R packagesCited by: 6
Author(s): Matti Vuorre, Matthew J. C. Crump
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pone.0237272
Passenger-surface microbiome interactions in the subway of Mexico CityCited by: 10
Author(s): Daniela Vargas-Robles, Carolina Gonzalez-Cedillo, Apolinar M. Hernández, Luis David Alcaraz, Mariana Peimbert
Software Mentions: 6
Published: over 4 years ago
10.1007/s00604-018-3195-6
A smartphone readout system for gold nanoparticle-based lateral flow assays: application to monitoring of digoxigeninCited by: 46
Author(s): Christoph Ruppert, Navneet Phogat, Stefan Laufer, Matthias Kohl, Hans‐Peter Deigner
Software Mentions: 6
Published: almost 6 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 studyCited 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 YipRCited by: 26
Author(s): Shi-Qi An, Miguel A. Valvano, Yu Yi, Jeremy S. Webb, Guillermo López–Campos
Software Mentions: 6
Published: almost 5 years ago
10.1093/g3journal/jkab040
<i>EnvRtype</i>: a software to interplay enviromics and quantitative genomics in agricultureCited by: 44
Author(s): Germano Costa‐Neto, Giovanni Galli, Humberto Fanelli Carvalho, J. Crossa, Roberto Fritsche‐Neto
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12859-019-2780-y
Focused multidimensional scaling: interactive visualization for exploration of high-dimensional dataCited by: 11
Author(s): Lea Urpa, Simon Anders
Software Mentions: 6
Published: over 5 years ago
10.2174/1874104501711010212
Ezqsar: An R Package for Developing QSAR Models Directly From StructuresCited by: 10
Author(s): Jamal Shamsara
Software Mentions: 6
Published: almost 7 years ago
10.1111/1755-0998.12676
<scp>treespace</scp> : Statistical exploration of landscapes of phylogenetic treesCited by: 131
Author(s): Thibaut Jombart, Michaela Kendall, Jacob Almagro-Garcia, Caroline Colijn
Software Mentions: 6
Published: over 7 years ago
10.7717/peerj-cs.520
<i>dxpr</i>: an R package for generating analysis-ready data from electronic health records—diagnoses and proceduresCited by: 2
Author(s): Yi-Ju Tseng, Hsiang Ju Chiu, Chun Ju Chen
Software Mentions: 6
Published: over 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 FungiCited by: 2
Author(s): Marco Chiapello, Debatosh Das, Caroline Gutjahr
Software Mentions: 6
Published: about 5 years ago
10.1038/s41598-017-06880-y
A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic FibrosisCited 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: over 7 years ago
10.7717/peerj.4402
Comparative genomic analysis of a new tellurite-resistant<i>Psychrobacter</i>strain isolated from the Antarctic PeninsulaCited 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: almost 7 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 trialsCited by: 2
Author(s): Casimir Ledoux Sofeu, Virginie Rondeau
Software Mentions: 5
Published: almost 5 years ago
10.3390/metabo8010016
RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and MetabolitesCited 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 linkageCited by: 7
Author(s): Shirlee Wohl, J. R. Giles, Justin Lessler
Software Mentions: 5
Published: over 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: over 7 years ago
10.1371/journal.pone.0121760
medplot: A Web Application for Dynamic Summary and Analysis of Longitudinal Medical Data Based on RCited by: 5
Author(s): Črt Ahlin, Daša Stupica, Franc Strle, Lara Lusa
Software Mentions: 5
Published: over 9 years ago