| Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 | 2014/12/01 | English | 43,694 |
| Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes | 2002/06/18 | English | 13,505 |
| Differential expression analysis for sequence count data | 2010/10/01 | English | 10,733 |
| Model-based Analysis of ChIP-Seq (MACS) | 2008/09/17 | English | 10,070 |
| DAVID: Database for Annotation, Visualization, and Integrated Discovery | 2003/04/03 | English | 5,728 |
| The Ensembl Variant Effect Predictor | 2016/06/06 | English | 3,777 |
| OrthoFinder: phylogenetic orthology inference for comparative genomics | 2019/11/14 | English | 2,559 |
| Kraken: ultrafast metagenomic sequence classification using exact alignments | 2014/03/03 | English | 2,498 |
| SCANPY: large-scale single-cell gene expression data analysis | 2018/02/06 | English | 2,486 |
| MicroRNA targets in Drosophila | 2003/12/12 | English | 2,303 |
| Improved metagenomic analysis with Kraken 2 | 2019/11/28 | English | 2,253 |
| xCell: digitally portraying the tissue cellular heterogeneity landscape | 2017/11/15 | English | 2,169 |
| GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers | 2011/04/01 | English | 2,107 |
| OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy | 2015/08/06 | English | 1,964 |
| Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression | 2019/12/01 | English | 1,627 |
| Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression | 2016/10/20 | English | 1,624 |
| Mash: fast genome and metagenome distance estimation using MinHash | 2016/06/20 | English | 1,488 |
| GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes | 2020/09/10 | English | 1,403 |
| MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data | 2015/12/01 | English | 1,367 |
| Comprehensive analyses of tumor immunity: implications for cancer immunotherapy | 2016/08/22 | English | 1,348 |
| Identifying biological themes within lists of genes with EASE | 2003/09/11 | English | 1,302 |
| A survey of best practices for RNA-seq data analysis | 2016/01/26 | English | 1,270 |
| HiC-Pro: an optimized and flexible pipeline for Hi-C data processing | 2015/12/01 | English | 1,207 |
| DAVID: Database for Annotation, Visualization, and Integrated Discovery | 2003/08/14 | English | 1,171 |
| MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens | 2014/12/01 | English | 1,129 |
| Multi-omics approaches to disease | 2017/05/05 | English | 1,124 |
| Expanded identification and characterization of mammalian circular RNAs | 2014/07/01 | English | 1,116 |
| Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation | 2004/02/16 | English | 1,076 |
| BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources | 2009/11/01 | English | 1,055 |
| The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes | 2014/11/01 | English | 1,044 |