| NIH Image to ImageJ: 25 years of image analysis | 2012/06/28 | English | 40,364 |
| Fiji: an open-source platform for biological-image analysis | 2012/06/28 | English | 36,660 |
| Fast gapped-read alignment with Bowtie 2 | 2012/03/04 | English | 31,549 |
| QIIME allows analysis of high-throughput community sequencing data | 2010/04/11 | English | 25,916 |
| DADA2: High-resolution sample inference from Illumina amplicon data | 2016/05/23 | English | 15,588 |
| SciPy 1.0: fundamental algorithms for scientific computing in Python | 2020/02/03 | English | 14,589 |
| HISAT: a fast spliced aligner with low memory requirements | 2015/03/09 | English | 12,598 |
| jModelTest 2: more models, new heuristics and parallel computing | 2012/07/30 | English | 12,009 |
| UPARSE: highly accurate OTU sequences from microbial amplicon reads | 2013/08/18 | English | 11,015 |
| Mapping and quantifying mammalian transcriptomes by RNA-Seq | 2008/05/30 | English | 9,593 |
| A method and server for predicting damaging missense mutations | 2010/04/01 | English | 9,445 |
| ModelFinder: fast model selection for accurate phylogenetic estimates | 2017/05/08 | English | 7,706 |
| SignalP 4.0: discriminating signal peptides from transmembrane regions | 2011/09/29 | English | 6,941 |
| Robust enumeration of cell subsets from tissue expression profiles | 2015/03/30 | English | 6,820 |
| Fast and sensitive protein alignment using DIAMOND | 2014/11/17 | English | 6,522 |
| Enzymatic assembly of DNA molecules up to several hundred kilobases | 2009/04/12 | English | 5,991 |
| Universal sample preparation method for proteome analysis | 2009/04/19 | English | 5,526 |
| Salmon provides fast and bias-aware quantification of transcript expression | 2017/03/06 | English | 5,225 |
| Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) | 2006/08/09 | English | 5,163 |
| The Perseus computational platform for comprehensive analysis of (prote)omics data | 2016/06/27 | English | 4,529 |
| MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy | 2017/02/27 | English | 4,436 |
| The I-TASSER Suite: protein structure and function prediction | 2014/12/30 | English | 4,029 |
| cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination | 2017/02/06 | English | 3,787 |
| Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position | 2013/10/06 | English | 3,729 |
| Improved vectors and genome-wide libraries for CRISPR screening | 2014/07/30 | English | 3,173 |
| CHARMM36m: an improved force field for folded and intrinsically disordered proteins | 2016/11/07 | English | 3,153 |
| Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data | 2013/05/05 | English | 3,124 |
| Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry | 2007/02/27 | English | 2,841 |
| Quantum dots versus organic dyes as fluorescent labels | 2008/08/28 | English | 2,835 |
| Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing | 2013/01/01 | English | 2,796 |