| 1 | phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data | PLoS ONE | 2013 | 15,210 |
| 2 | FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments | PLoS ONE | 2010 | 10,556 |
| 3 | Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement | PLoS ONE | 2014 | 6,068 |
| 4 | A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species | PLoS ONE | 2011 | 4,666 |
| 5 | REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms | PLoS ONE | 2011 | 4,591 |
| 6 | Leishmaniasis Worldwide and Global Estimates of Its Incidence | PLoS ONE | 2012 | 3,823 |
| 7 | Plastic Pollution in the World's Oceans: More than 5 Trillion Plastic Pieces Weighing over 250,000 Tons Afloat at Sea | PLoS ONE | 2014 | 3,245 |
| 8 | SoilGrids250m: Global gridded soil information based on machine learning | PLoS ONE | 2017 | 3,053 |
| 9 | BrainNet Viewer: A Network Visualization Tool for Human Brain Connectomics | PLoS ONE | 2013 | 2,997 |
| 10 | progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement | PLoS ONE | 2010 | 2,903 |
| 11 | Global Prevalence of Chronic Kidney Disease – A Systematic Review and Meta-Analysis | PLoS ONE | 2016 | 2,755 |
| 12 | Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species | PLoS ONE | 2012 | 2,734 |
| 13 | Dose-Response Analysis Using R | PLoS ONE | 2015 | 2,702 |
| 14 | The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets | PLoS ONE | 2015 | 2,663 |
| 15 | Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers | PLoS ONE | 2008 | 2,465 |
| 16 | Source Partitioning Using Stable Isotopes: Coping with Too Much Variation | PLoS ONE | 2010 | 2,386 |
| 17 | Yield Trends Are Insufficient to Double Global Crop Production by 2050 | PLoS ONE | 2013 | 2,220 |
| 18 | Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults | PLoS ONE | 2010 | 2,209 |
| 19 | NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data | PLoS ONE | 2012 | 2,197 |
| 20 | More than 75 percent decline over 27 years in total flying insect biomass in protected areas | PLoS ONE | 2017 | 2,171 |
| 21 | Predicting the Functional Effect of Amino Acid Substitutions and Indels | PLoS ONE | 2012 | 2,162 |
| 22 | SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation | PLoS ONE | 2016 | 2,040 |
| 23 | On Pixel-Wise Explanations for Non-Linear Classifier Decisions by Layer-Wise Relevance Propagation | PLoS ONE | 2015 | 2,001 |
| 24 | An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets | PLoS ONE | 2007 | 1,998 |
| 25 | Graphical Tools for Network Meta-Analysis in STATA | PLoS ONE | 2013 | 1,950 |
| 26 | Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types | PLoS ONE | 2012 | 1,921 |
| 27 | pRRophetic: An R Package for Prediction of Clinical Chemotherapeutic Response from Tumor Gene Expression Levels | PLoS ONE | 2014 | 1,835 |
| 28 | A simple method to assess and report thematic saturation in qualitative research | PLoS ONE | 2020 | 1,765 |
| 29 | Future Coastal Population Growth and Exposure to Sea-Level Rise and Coastal Flooding - A Global Assessment | PLoS ONE | 2015 | 1,754 |
| 30 | Mental health problems and social media exposure during COVID-19 outbreak | PLoS ONE | 2020 | 1,744 |
| 31 | A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System | PLoS ONE | 2013 | 1,734 |
| 32 | ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software | PLoS ONE | 2014 | 1,720 |
| 33 | Racism as a Determinant of Health: A Systematic Review and Meta-Analysis | PLoS ONE | 2015 | 1,711 |
| 34 | Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies | PLoS ONE | 2011 | 1,684 |
| 35 | Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation | PLoS ONE | 2010 | 1,675 |
| 36 | REST: A Toolkit for Resting-State Functional Magnetic Resonance Imaging Data Processing | PLoS ONE | 2011 | 1,652 |
| 37 | Singularity: Scientific containers for mobility of compute | PLoS ONE | 2017 | 1,625 |
| 38 | A One Pot, One Step, Precision Cloning Method with High Throughput Capability | PLoS ONE | 2008 | 1,588 |
| 39 | A Meta-Analysis of Global Urban Land Expansion | PLoS ONE | 2011 | 1,576 |
| 40 | SRplot: A free online platform for data visualization and graphing | PLoS ONE | 2023 | 1,553 |
| 41 | In Silico Approach for Predicting Toxicity of Peptides and Proteins | PLoS ONE | 2013 | 1,508 |
| 42 | The Biodiversity of the Mediterranean Sea: Estimates, Patterns, and Threats | PLoS ONE | 2010 | 1,494 |
| 43 | The Role of Google Scholar in Evidence Reviews and Its Applicability to Grey Literature Searching | PLoS ONE | 2015 | 1,492 |
| 44 | The Increasing Trend in Caesarean Section Rates: Global, Regional and National Estimates: 1990-2014 | PLoS ONE | 2016 | 1,453 |
| 45 | Using and Reporting the Delphi Method for Selecting Healthcare Quality Indicators: A Systematic Review | PLoS ONE | 2011 | 1,428 |
| 46 | cocor: A Comprehensive Solution for the Statistical Comparison of Correlations | PLoS ONE | 2015 | 1,427 |
| 47 | Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer | PLoS ONE | 2013 | 1,392 |
| 48 | Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach | PLoS ONE | 2012 | 1,353 |
| 49 | Homogenous 96-Plex PEA Immunoassay Exhibiting High Sensitivity, Specificity, and Excellent Scalability | PLoS ONE | 2014 | 1,342 |
| 50 | The Smartphone Addiction Scale: Development and Validation of a Short Version for Adolescents | PLoS ONE | 2013 | 1,317 |
