cran: tidyr | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1007912

bigPint: A Bioconductor visualization package that makes big data pint-sized
Cited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago

Revisiting potential associations between brain morphology, fear acquisition and extinction through new data and a literature review
Cited by: 7
Author(s): Mana R. Ehlers, Janne Nold, Manuel Kuhn, Maren Klingelhöfer-Jens, Tina B. Lonsdorf
Software Mentions: 44
Published: about 4 years ago

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: almost 5 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: over 6 years ago

10.3389/fonc.2020.617890

Comparative Proteome Identifies Complement Component 3-Mediated Immune Response as Key Difference of Colon Adenocarcinoma and Rectal Adenocarcinoma
Cited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: almost 4 years ago

10.1038/s41598-019-54004-5

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates
Cited by: 61
Author(s): Arun Gonzales Decano, Tim Downing
Software Mentions: 30
Published: about 5 years ago

10.1371/journal.pcbi.1005752

mixOmics: An R package for ‘omics feature selection and multiple data integration
Cited by: 1,902
Author(s): Florian Rohart, Benoît Gautier, Amrit Singh, Kim‐Anh Lê Cao
Software Mentions: 29
Published: about 7 years ago

10.1084/jem.20210915

Blood transcriptomics reveal the evolution and resolution of the immune response in tuberculosis
Cited by: 27
Author(s): Olivier Tabone, Raman Verma, Akul Singhania, Probir Chakravarty, William J. Branchett, Christine M. Graham, Jo Lee, Trần Thị Huyền Trang, Frédéric Reynier, Philippe Leissner, Karine Kaiser, Marc Rodrigue, Gerrit Woltmann, Pranabashis Haldar, Anne O’Garra
Software Mentions: 27
Published: over 3 years ago

10.3390/microorganisms9051094

Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance
Cited by: 16
Author(s): Alfredo Mari, Tim Roloff, Madlen Stange, Kirstine Kobberøe Søgaard, Erblin Asllanaj, Gerardo Tauriello, Leila T. Alexander, Michael Schweitzer, Karoline Leuzinger, Alexander Gensch, Aurélien Emmanuel Martinez, Julia Bielicki, Hans Pargger, Martin Siegemund, Christian H. Nickel, Roland Bingisser, Michael Osthoff, Stefano Bassetti, Parham Sendi, Manuel Battegay, Catia Marzolini, Helena M. B. Seth-Smith, Torsten Schwede, Hans H. Hirsch, Adrian Egli
Software Mentions: 27
Published: over 3 years ago

10.3390/s20247188

Which Are the Central Aspects of Infant Sleep? The Dynamics of Sleep Composites across Infancy
Cited by: 17
Author(s): Sarah F. Schoch, Reto Huber, Malcolm Kohler, Salomé Kurth
Software Mentions: 26
Published: about 4 years ago

10.1111/joa.13366

Selection on vocal output affects laryngeal morphology in rats
Cited by: 6
Author(s): Raffaela Lesch, Thomas Schwaha, Andrea Orozco, Margaret Shilling, Susan A. Brunelli, Myron A. Hofer, Daniel L. Bowling, Betty Zimmerberg, W. Tecumseh Fitch
Software Mentions: 25
Published: almost 4 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: over 4 years ago

10.3389/fimmu.2021.616967

A Multi-Omics Analysis of Mucosal-Associated-Invariant T Cells Reveals Key Drivers of Distinct Modes of Activation
Cited by: 12
Author(s): Kristin Schubert, Isabel Karkossa, Jana Schor, Beatrice Engelmann, Lisa Maria Steinheuer, Tony Bruns, Ulrike Rolle-Kampczyk, Jörg Hackermüller, Martin von Bergen
Software Mentions: 24
Published: over 3 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: almost 5 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: about 4 years ago

10.3389/fimmu.2021.701085

A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients
Cited by: 29
Author(s): Florian Bieberich, Rodrigo Vazquez-Lombardi, Alexander Yermanos, Roy Ehling, Derek M Mason, Bastian Wagner, Edo Kapetanovic, Raphaël Brisset Di Roberto, Cédric R. Weber, Miodrag Savic, Fabian Rudolf, Sai T. Reddy
Software Mentions: 23
Published: over 3 years ago

10.7554/eLife.70086

Gaps in global wildlife trade monitoring leave amphibians vulnerable
Cited by: 22
Author(s): Alice C. Hughes, Benjamin Michael Marshall, Colin Thomas Strine
Software Mentions: 23
Published: over 3 years ago

10.3390/cells8091045

Systematic Assessment of Blood-Borne MicroRNAs Highlights Molecular Profiles of Endurance Sport and Carbohydrate Uptake
Cited by: 12
Author(s): Fabian Kern, Nicole Ludwig, Christina Backes, Esther Maldener, Tobias Fehlmann, Artur Suleymanov, Eckart Meese, Anne Hecksteden, Andreas Keller, Tim Meyer
Software Mentions: 21
Published: over 5 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

10.7717/peerj.4278

Forecasting biodiversity in breeding birds using best practices
Cited by: 37
Author(s): David J. Harris, Shawn D. Taylor, Ethan P. White
Software Mentions: 21
Published: almost 7 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: over 4 years ago

10.1016/j.csbj.2019.10.003

MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines
Cited by: 9
Author(s): Wei Zhou, Lei Wang, Wenming Zheng, Wen Yao
Software Mentions: 20
Published: almost 6 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: about 6 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: almost 6 years ago

10.1155/2021/6613151

Genomic and Transcriptome Analysis to Identify the Role of the mTOR Pathway in Kidney Renal Clear Cell Carcinoma and Its Potential Therapeutic Significance
Cited by: 6
Author(s): Xiangyu Che, Xiaochen Qi, Yingkun Xu, Qifei Wang, Guangzhen Wu
Software Mentions: 19
Published: over 3 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: about 4 years ago

10.1186/s40168-019-0702-x

Understanding microbial community dynamics to improve optimal microbiome selection
Cited by: 193
Author(s): Robyn J. Wright, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 18
Published: over 5 years ago

10.3390/cancers13102419

Deep Learning for the Classification of Non-Hodgkin Lymphoma on Histopathological Images
Cited by: 16
Author(s): Georg Steinbuß, Mark Kriegsmann, Christiane Zgorzelski, Alexander Brobeil, Benjamin Goeppert, Sascha Dietrich, Gunhild Mechtersheimer, Katharina Kriegsmann
Software Mentions: 18
Published: over 3 years ago

10.3389/fimmu.2021.620270

Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaP
Cited by: 18
Author(s): Henning Großkopf, Katharina Walter, Isabel Karkossa, Martin von Bergen, Kristin Schubert
Software Mentions: 18
Published: over 3 years ago

10.1186/s12859-019-3059-z

HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data
Cited by: 28
Author(s): Anh Tran, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, Anita B. Hjelmeland
Software Mentions: 18
Published: over 5 years ago

10.3390/ijms22105385

Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma
Cited by: 15
Author(s): Mark Kriegsmann, Katharina Kriegsmann, Georg Steinbuß, Christiane Zgorzelski, Anne Kraft, Matthias M. Gaida
Software Mentions: 18
Published: over 3 years ago

10.3390/genes12030413

Spt4 Promotes Pol I Processivity and Transcription Elongation
Cited by: 5
Author(s): Abigail K. Huffines, Yvonne J. K. Edwards, David A. Schneider
Software Mentions: 18
Published: almost 4 years ago

10.1371/journal.pone.0238665

Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains
Cited by: 19
Author(s): Anastasis Oulas, Maria Zanti, Marios Tomazou, Margarita Zachariou, George Minadakis, Marilena M. Bourdakou, Margarita Zachariou, George M. Spyrou
Software Mentions: 18
Published: almost 4 years ago

10.3390/brainsci11081017

Facial Signals and Social Actions in Multimodal Face-to-Face Interaction
Cited by: 14
Author(s): Naomi Nota, James P. Trujillo, Judith Holler
Software Mentions: 17
Published: over 3 years ago

10.1038/s42003-021-02025-0

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy
Cited by: 23
Author(s): Marta Giovanetti, Eleonora Cella, Francesca Benedetti, Brittany Rife Magalis, Vagner Fonseca, Silvia Fabris, Giovanni Campisi, Alessandra Ciccozzi, Silvia Angeletti, Alessândra Borsetti, Vittoradolfo Tambone, Caterina Sagnelli, Stefano Pascarella, Alberto Riva, Giancarlo Ceccarelli, Alessandro Marcello, Taj Azarian, Eduan Wilkinson, Túlio de Oliveira, Luiz Carlos Júnior Alcântara, Roberto Cauda, Arnaldo Caruso, Natalie E. Dean, Cameron J. Browne, José Lourenço, Marco Salemi, Davide Zella, Massimo Ciccozzi
Software Mentions: 17
Published: over 3 years ago

10.1001/jamanetworkopen.2020.37227

Trends in US Pediatric Hospital Admissions in 2020 Compared With the Decade Before the COVID-19 Pandemic
Cited by: 115
Author(s): Jonathan Pelletier, Jaskaran Rakkar, Alicia K. Au, Dana Y. Fuhrman, Robert S. B. Clark, Christopher M. Horvat
Software Mentions: 17
Published: almost 4 years ago

10.1186/s12859-020-03577-4

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago

10.1016/j.cell.2019.12.013

Identification of a Master Regulator of Differentiation in Toxoplasma
Cited by: 154
Author(s): Benjamin S. Waldman, Dominic Schwarz, Marc H. Wadsworth, Jeroen P. J. Saeij, Alex K. Shalek, Sebastian Lourido
Software Mentions: 17
Published: almost 5 years ago

10.3389/fvets.2021.620327

Detection of Mycobacterium avium ssp. paratuberculosis in Cultures From Fecal and Tissue Samples Using VOC Analysis and Machine Learning Tools
Cited by: 6
Author(s): Philipp Vitense, Elisa Kasbohm, Anne Klassen, Peter Gierschner, Phillip Trefz, M. Weber, Wolfram Miekisch, Jochen K. Schubert, Petra Möbius, Petra Reinhold, Volkmar Liebscher, Heike Köhler
Software Mentions: 17
Published: almost 4 years ago

10.1186/s13059-019-1819-8

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Cited by: 12
Author(s): Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett, Daniel Brewer
Software Mentions: 17
Published: about 5 years ago

10.3389/fmicb.2019.00240

Changes in Trophic Groups of Protists With Conversion of Rainforest Into Rubber and Oil Palm Plantations
Cited by: 38
Author(s): Garvin Schulz, Dominik Schneider, Nicole Brinkmann, Nur Edy, Rolf Daniel, Andrea Polle, Stefan Scheu, Valentyna Krashevska
Software Mentions: 16
Published: almost 6 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/cells10092367

The Emerging Plasticizer Alternative DINCH and Its Metabolite MINCH Induce Oxidative Stress and Enhance Inflammatory Responses in Human THP-1 Macrophages
Cited by: 16
Author(s): Alexandra Schaffert, Josi Arnold, Isabel Karkossa, Matthias Blüher, Martin von Bergen, Kristin Schubert
Software Mentions: 16
Published: over 3 years ago

10.1126/sciimmunol.abd6832

Natural killer cell immunotypes related to COVID-19 disease severity
Cited by: 315
Author(s): Christopher Maucourant, Iva Filipovic, Andrea Ponzetta, Soo Aleman, Martin Cornillet, Laura Hertwig, Benedikt Strunz, Antonio Lentini, Björn Reinius, Demi Brownlie, Angélica Cuapio, Eivind Heggernes Ask, Ryan M. Hull, Alvaro Haroun-Izquierdo, Marie Schaffer, Jonas Klingström, Elin Folkesson, Marcus Buggert, Johan K. Sandberg, Lars Eriksson, Olav Rooyackers, Hans‐Gustaf Ljunggren, Karl‐Johan Malmberg, Jakob Michaëlsson, Nicole Marquardt, Quirin Hammer, Kristoffer Strålin, Niklas K. Björkström
Software Mentions: 16
Published: over 4 years ago

10.7554/eLife.61812

Reproducible analysis of disease space via principal components using the novel R package syndRomics
Cited by: 18
Author(s): Abel Torres-Espín, Austin Chou, J. Russell Huie, Nikos Kyritsis, Pavan S. Upadhyayula, Adam R. Ferguson
Software Mentions: 16
Published: almost 4 years ago

10.3390/cancers13123089

A Comprehensive Bioinformatics Analysis of Notch Pathways in Bladder Cancer
Cited by: 12
Author(s): Chuan Zhang, Mandy Berndt‐Paetz, Jochen Neuhaus
Software Mentions: 15
Published: over 3 years ago

10.3389/fgene.2021.559998

Gene Size Matters: An Analysis of Gene Length in the Human Genome
Cited by: 55
Author(s): Inês Lopes, Gulam Altab, Priyanka Raina, João Pedro de Magalhães
Software Mentions: 15
Published: almost 4 years ago

10.1371/journal.pone.0219892

Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating
Cited by: 18
Author(s): Marianna Karava, Felix Bracharz, Johannes Kabisch
Software Mentions: 15
Published: over 5 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: over 6 years ago

10.1038/s41598-020-63428-3

No evidence of spontaneous preference for slowly moving objects in visually naïve chicks
Cited by: 7
Author(s): Bastien S. Lemaire
Software Mentions: 15
Published: over 4 years ago

10.1186/s12859-020-03860-4

Finding a suitable library size to call variants in RNA-Seq
Cited by: 3
Author(s): Anna Quaglieri, Christoffer Flensburg, Terence P. Speed, Ian J. Majewski
Software Mentions: 15
Published: about 4 years ago

10.1007/s43032-020-00438-6

Changes in the Vaginal Microbiome during the Pregnancy to Postpartum Transition
Cited by: 24
Author(s): Kenetta L. Nunn, Steven S. Witkin, Gudrun Schneider, Allison Boester, Dimitrios Nasioudis, Evelyn Minis, Karol Gliniewicz, Larry J. Forney
Software Mentions: 14
Published: almost 4 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: over 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: about 4 years ago

10.3390/cells10030620

Measuring Pre- and Post-Copulatory Sexual Selection and Their Interaction in Socially Monogamous Species with Extra-Pair Paternity
Cited by: 6
Author(s): Emily R. A. Cramer
Software Mentions: 14
Published: almost 4 years ago

10.3389/fpsyg.2020.564083

Correlates of Health-Protective Behavior During the Initial Days of the COVID-19 Outbreak in Norway
Cited by: 54
Author(s): Janis Zickfeld, Thomas W. Schubert, Anders Kuvaas Herting, Jon Grahe, Kate Faasse
Software Mentions: 14
Published: about 4 years ago

10.3758/s13420-020-00446-1

Response of male and female domestic chicks to change in the number (quantity) of imprinting objects
Cited by: 5
Author(s): Bastien S. Lemaire, Rosa Rugani, Lucia Regolin, Giorgio Vallortígara
Software Mentions: 14
Published: about 4 years ago

10.3389/fimmu.2020.572924

Differential Skewing of Circulating MR1-Restricted and γδ T Cells in Human Psoriasis Vulgaris
Cited by: 7
Author(s): Vera Plužarić, Mario Štefanić, Martina Mihalj, Maja Tolušić Levak, Ivanka Muršić, Ljubica Glavaš‐Obrovac, Martin Petřek, Péter Balogh, Stana Tokić
Software Mentions: 14
Published: about 4 years ago

10.1371/journal.pcbi.1005158

Machine Learning for Characterization of Insect Vector Feeding
Cited by: 25
Author(s): Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski, Stephen L. Lapointe
Software Mentions: 14
Published: about 8 years ago

10.3389/fonc.2020.575422

A Novel Model Based on CXCL8-Derived Radiomics for Prognosis Prediction in Colorectal Cancer
Cited by: 8
Author(s): Yanpeng Chu, Jie Li, Zong Yuan Zeng, Bin Huang, Jiaojiao Zhao, Qin Liu, Huaping Wu, Jiangping Fu, Zheng Yin, Yefan Zhang, Jianqiang Cai, Fanxin Zeng
Software Mentions: 14
Published: about 4 years ago

10.1371/journal.pbio.3000581

PlotTwist: A web app for plotting and annotating continuous data
Cited by: 43
Author(s): Joachim Goedhart
Software Mentions: 14
Published: almost 5 years ago

10.7150/jca.55970

Characteristics of Infiltrating Immune Cells and a Predictive Immune Model for Cervical Cancer
Cited by: 11
Author(s): Ruanmin Zou, Ruihong Gu, Xinbing Yu, Yingying Hu, Ji Hee Yu, Xiangyang Xue, Xueqiong Zhu
Software Mentions: 14
Published: almost 4 years ago

10.7717/peerj.4729

Effects of nettle slurry (<i>Urtica dioica</i> L.) used as foliar fertilizer on potato (<i>Solanum tuberosum</i> L.) yield and plant growth
Cited by: 9
Author(s): Alfonso Garmendia, María Dolores Raigón, Olmo Marques, M. Ferriol, Jorge Royo, Hugo Merlé
Software Mentions: 14
Published: over 6 years ago

10.1186/s12920-017-0274-1

Quantitative analysis of cryptic splicing associated with TDP-43 depletion
Cited by: 74
Author(s): Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs, Vincent Plagnol
Software Mentions: 14
Published: over 7 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: about 5 years ago

10.3390/ijms20174162

SILAC-Based Quantification of TGFBR2-Regulated Protein Expression in Extracellular Vesicles of Microsatellite Unstable Colorectal Cancers
Cited by: 13
Author(s): Fabia Fricke, Malwina Michalak, Uwe Warnken, Ingrid Haußer, Martina Schnölzer, Jürgen Kopitz, Johannes Gebert
Software Mentions: 14
Published: over 5 years ago

10.1093/gigascience/giab039

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Cited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: over 3 years ago

10.1186/s13059-019-1783-3

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
Cited by: 20
Author(s): Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin, Katherine S. Pollard
Software Mentions: 14
Published: over 5 years ago

10.1038/s41598-021-97071-3

Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L.) from pre-sowing to post-harvest of crop under field conditions
Cited by: 10
Author(s): Ankit T. Hinsu, Ketankumar Panchal, Ramesh Pandit, Prakash G. Koringa, Ramesh Kothari
Software Mentions: 14
Published: over 3 years ago

10.1186/s13072-020-00343-x

BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
Cited by: 29
Author(s): Lőrinc Sándor Pongor, Jacob M. Gross, Roberto Vera Alvarez, Junko Murai, Sang‐Min Jang, Hongliang Zhang, Christophe E. Redon, Haiqing Fu, Shar-yin N. Huang, Bhushan Thakur, Adrian Baris, Leonardo Mariño‐Ramírez, David Landsman, Mirit I. Aladjem, Yves Pommier
Software Mentions: 13
Published: over 4 years ago

10.1186/s12859-020-03922-7

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
Cited by: 3
Author(s): Krutika S. Gaonkar, Fédérico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam Resnick, Konstantin Strauch, Jaclyn N. Taroni, Jo Lynne Rokita
Software Mentions: 13
Published: about 4 years ago

10.3389/fmicb.2020.02028

Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn’s Disease and Ulcerative Colitis
Cited by: 8
Author(s): Jake C. Szamosi, Jessica D. Forbes, John W. Copeland, Natalie Knox, Shahrokh Shekarriz, Laura Rossi, Morag Graham, Christine Bonner, David S. Guttman, Gary Van Domselaar, Michael G. Surette, Çharles N. Bernstein
Software Mentions: 13
Published: over 4 years ago

10.7554/eLife.57116

shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
Cited by: 35
Author(s): Kenichi Shimada, John A. Bachman, Jeremy Muhlich, Timothy J. Mitchison
Software Mentions: 13
Published: almost 4 years ago

10.3389/fmicb.2021.689262

Monitoring of Antimicrobial Resistance to Aminoglycosides and Macrolides in Campylobacter coli and Campylobacter jejuni From Healthy Livestock in Spain (2002–2018)
Cited by: 9
Author(s): Vicente Lopez-Chavarrias, María Ugarte‐Ruiz, Carmen Bárcena, Adolfo Olarra, María Teresa Antonio García, José Luís Saez, Cristina de Frutos, Tania Serrano, I. Abad Perez, M. Moreno, Lucas Domı́nguez, Julio Álvarez
Software Mentions: 13
Published: over 3 years ago

10.2196/mental.9946

Predicting Caller Type From a Mental Health and Well-Being Helpline: Analysis of Call Log Data
Cited by: 9
Author(s): Alexander Grigorash, Siobhan O’Neill, Raymond Bond, Colette Ramsey, Chérie Armour, Maurice Mulvenna
Software Mentions: 13
Published: over 6 years ago

10.1186/s13059-020-02233-7

tidybulk: an R tidy framework for modular transcriptomic data analysis
Cited by: 22
Author(s): Stefano Mangiola, Ramyar Molania, Ruining Dong, Maria A. Doyle, Anthony T. Papenfuss
Software Mentions: 13
Published: almost 4 years ago

10.1371/journal.pone.0159046

Accuracy and Calibration of Computational Approaches for Inpatient Mortality Predictive Modeling
Cited by: 13
Author(s): Christos T. Nakas, Narayan Schütz, Marcus Werners, Alexander Benedikt Leichtle
Software Mentions: 13
Published: over 8 years ago

10.3389/fimmu.2020.620716

Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help
Cited by: 14
Author(s): Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Xuefeng Gao, Fabien Crauste, Philippe A. Robert, Michael Meyer‐Hermann, María Rodríguez Martínez, S. Marieke van Ham, Jeroen E. J. Guikema, Huub Hoefsloot, Antoine H. C. van Kampen
Software Mentions: 13
Published: almost 4 years ago

10.1371/journal.pone.0178783

Pharmacokinetics of caspofungin acetate to guide optimal dosing in cats
Cited by: 8
Author(s): Jana Leshinsky, Andrew J. McLachlan, David J. R. Foster, Ross Norris, Vanessa R. Barrs
Software Mentions: 13
Published: over 7 years ago

10.3389/fcell.2021.709022

Identification of the Role and Clinical Prognostic Value of Target Genes of m6A RNA Methylation Regulators in Glioma
Cited by: 24
Author(s): Peilin Cong, Tingmei Wu, Xinwei Huang, Huazheng Liang, Xiaofei Gao, Li Tian, Wanrong Li, Aiwen Chen, Hanxi Wan, Mengfan He, Danqing Dai, Zhen Li, Lize Xiong
Software Mentions: 13
Published: over 3 years ago

10.1002/ece3.5586

Life history alterations upon oral and hemocoelic bacterial exposure in the butterfly Melitaea cinxia
Cited by: 1
Author(s): Luisa Woestmann, Dimitri Stucki, Marjo Saastamoinen
Software Mentions: 13
Published: over 5 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: almost 4 years ago

10.1002/jgh3.12451

Presence and type of decompensation affects outcomes in autoimmune hepatitis upon treatment with corticosteroids
Cited by: 1
Author(s): Sanchit Sharma, Samagra Agarwal, Kanica Kaushal, Abhinav Anand, Deepak Gunjan, Rajni Yadav, Sanchit Sharma
Software Mentions: 13
Published: about 4 years ago

10.1038/s41598-021-86989-3

Stability and individual variability of social attachment in imprinting
Cited by: 15
Author(s): Bastien S. Lemaire, Daniele Rucco, Mathilde Josserand, Giorgio Vallortígara, Elisabetta Versace
Software Mentions: 12
Published: over 3 years ago

10.1186/s41073-017-0030-2

Concern noted: a descriptive study of editorial expressions of concern in PubMed and PubMed Central
Cited by: 15
Author(s): Melissa Vaught, Diana C. Jordan, Hilda Bastian
Software Mentions: 12
Published: over 7 years ago

10.3390/metabo7020030

Evaluation of Classifier Performance for Multiclass Phenotype Discrimination in Untargeted Metabolomics
Cited by: 33
Author(s): Patrick J. Trainor, Andrew P. DeFilippis, N. Shesh
Software Mentions: 12
Published: over 7 years ago

10.1016/j.immuni.2021.05.010

Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease
Cited by: 188
Author(s): Laura Bergamaschi, Federica Mescia, Lorinda Turner, Aimee L. Hanson, Prasanti Kotagiri, Benjamin J. Dunmore, Hélène Ruffieux, Aloka De, Oisín Huhn, Michael D. Morgan, Pehuén Pereyra Gerber, Mark R. Wills, Stephen Baker, Fernando J Calero-Nieto, Rainer Döffinger, Gordon Dougan, Anne Elmer, Ian Goodfellow, Ravindra Gupta, Myra Hosmillo, Kelvin Hunter, Nathalie Kingston, Paul J. Lehner, Nicholas J Matheson, Jeremy K. Nicholson, A. M. Petrunkina, Sylvia Richardson, Caroline Saunders, James Thaventhiran, Erik J. M. Toonen, Michael P. Weekes, Berthold Göttgens, Mark Toshner, Christoph Hess, John R. Bradley, Paul Lyons, Kenneth Smith
Software Mentions: 12
Published: over 3 years ago

10.26508/lsa.202000770

In vivo CRISPR/Cas9 knockout screen: TCEAL1 silencing enhances docetaxel efficacy in prostate cancer
Cited by: 12
Author(s): Linda Rushworth, Victoria Harle, Peter Repiščák, William Clark, Robin Shaw, Holly Hall, Martin Bushell, Hing Y. Leung, Rachana Patel
Software Mentions: 12
Published: about 4 years ago

10.1186/s12998-019-0261-z

Concurrent validity of lower extremity kinematics and jump characteristics captured in pre-school children by a markerless 3D motion capture system
Cited by: 23
Author(s): Steen Harsted, Anders Holsgaard-Larsen, Lise Hestbæk, Eleanor Boyle, Henrik Hein Lauridsen
Software Mentions: 12
Published: over 5 years ago

10.1371/journal.pone.0205742

The calm during the storm: Snowfall events decrease the movement rates of grey wolves (Canis lupus)
Cited by: 10
Author(s): Amanda Droghini, Stan Boutin
Software Mentions: 12
Published: about 6 years ago

10.1371/journal.pone.0156293

Cryopreservation of Human Mucosal Leukocytes
Cited by: 14
Author(s): Sean M. Hughes, Zhiquan Shu, Claire Levy, April L. Ferre, Heather Hartig, Cifeng Fang, Gretchen M. Lentz, Michael Fialkow, Anna C. Kirby, Kristina M. Adams Waldorf, Ronald S. Veazey, Anja Germann, Hagen von Briesen, M. Juliana McElrath, Charlene S. Dezzutti, Elizabeth Sinclair, Chris A. R. Baker, Barbara L. Shacklett, Dayong Gao, Florian Hladik
Software Mentions: 12
Published: over 8 years ago

10.3389/fnut.2021.642612

The Association of Meat Intake With All-Cause Mortality and Acute Myocardial Infarction Is Age-Dependent in Patients With Stable Angina Pectoris
Cited by: 2
Author(s): Åslaug Oddsdatter Matre, Anthea Van Parys, Trond E. Olsen, Teresa Haugsgjerd, Carl Michael Baravelli, Ottar Nygård, Jutta Dierkes, Vegard Lysne
Software Mentions: 12
Published: almost 4 years ago

10.1093/aobpla/plz054

tealeaves: an R package for modelling leaf temperature using energy budgets
Cited by: 26
Author(s): Christopher D. Muir
Software Mentions: 12
Published: about 5 years ago

10.3390/toxins12070433

Low Doses of Mycotoxin Mixtures below EU Regulatory Limits Can Negatively Affect the Performance of Broiler Chickens: A Longitudinal Study
Cited by: 26
Author(s): Oluwatobi Kolawole, A. Graham, Caroline Julie Donaldson, B. Owens, Wilfred A. Abia, Julie Meneely, M. Alcorn, Lisa Connolly, Chris Elliott
Software Mentions: 12
Published: over 4 years ago

10.3390/diagnostics10020066

Identification of Key Biomarkers in Bladder Cancer: Evidence from a Bioinformatics Analysis
Cited by: 22
Author(s): Chuan Zhang, Mandy Berndt‐Paetz, Jochen Neuhaus
Software Mentions: 12
Published: almost 5 years ago

10.1371/journal.pone.0244005

DDRP: Real-time phenology and climatic suitability modeling of invasive insects
Cited by: 13
Author(s): Brittany S. Barker, Leonard B. Coop, Tyson Wepprich, Fritzi S. Grevstad, Gericke Cook
Software Mentions: 12
Published: almost 4 years ago

10.1186/s12889-021-11065-4

Who or what is to blame? Examining sociodemographic relationships to beliefs about causes, control, and responsibility for cancer and chronic disease prevention in Alberta, Canada
Cited by: 5
Author(s): Kimberley D. Curtin, Mathew Thomson, Candace I. J. Nykiforuk
Software Mentions: 12
Published: over 3 years ago

10.3389/fnbeh.2021.675994

Resurgence of an Inborn Attraction for Animate Objects via Thyroid Hormone T3
Cited by: 8
Author(s): Elena Lorenzi, Bastien S. Lemaire, Elisabetta Versace, Toshiya Matsushima, Giorgio Vallortígara
Software Mentions: 12
Published: over 3 years ago

10.4269/ajtmh.20-0757

A Computational Modeling Study of COVID-19 in Bangladesh
Cited by: 7
Author(s): Irtesam Mahmud Khan, Ubydul Haque, Samiha Kaisar, Md. Saidur Rahman
Software Mentions: 12
Published: almost 4 years ago

10.1371/journal.pone.0239197

Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures
Cited by: 13
Author(s): Weston R. Bodily, Brian H. Shirts, Tom Walsh, Süleyman Gülsüner, Mary‐Claire King, Alyssa Parker, Moom R. Roosan, Stephen R. Piccolo
Software Mentions: 12
Published: about 4 years ago

Projects: cran: tidyr

Papers Mentioning tidyr 321