# | Title | Journal | Year | Citations |
---|
1 | Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 | Genome Biology | 2014 | 58,325 |
2 | Differential expression analysis for sequence count data | Genome Biology | 2010 | 13,707 |
3 | DAVID: Database for Annotation, Visualization, and Integrated Discovery | Genome Biology | 2003 | 7,168 |
4 | The Ensembl Variant Effect Predictor | Genome Biology | 2016 | 5,181 |
5 | DAVID: Database for Annotation, Visualization, and Integrated Discovery | Genome Biology | 2003 | 4,682 |
6 | SCANPY: large-scale single-cell gene expression data analysis | Genome Biology | 2018 | 3,958 |
7 | OrthoFinder: phylogenetic orthology inference for comparative genomics | Genome Biology | 2019 | 3,367 |
8 | Improved metagenomic analysis with Kraken 2 | Genome Biology | 2019 | 2,909 |
9 | OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy | Genome Biology | 2015 | 2,812 |
10 | xCell: digitally portraying the tissue cellular heterogeneity landscape | Genome Biology | 2017 | 2,572 |
11 | GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers | Genome Biology | 2011 | 2,546 |
12 | Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression | Genome Biology | 2019 | 2,460 |
13 | Mash: fast genome and metagenome distance estimation using MinHash | Genome Biology | 2016 | 2,099 |
14 | MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data | Genome Biology | 2015 | 2,047 |
15 | Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression | Genome Biology | 2016 | 1,980 |
16 | Performance of neural network basecalling tools for Oxford Nanopore sequencing | Genome Biology | 2019 | 1,971 |
17 | A survey of best practices for RNA-seq data analysis | Genome Biology | 2016 | 1,898 |
18 | Comprehensive analyses of tumor immunity: implications for cancer immunotherapy | Genome Biology | 2016 | 1,768 |
19 | Identifying biological themes within lists of genes with EASE | Genome Biology | 2003 | 1,664 |
20 | HiC-Pro: an optimized and flexible pipeline for Hi-C data processing | Genome Biology | 2015 | 1,632 |
21 | MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens | Genome Biology | 2014 | 1,614 |
22 | GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes | Genome Biology | 2020 | 1,538 |
23 | Opportunities and challenges in long-read sequencing data analysis | Genome Biology | 2020 | 1,536 |
24 | Multi-omics approaches to disease | Genome Biology | 2017 | 1,439 |
25 | The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes | Genome Biology | 2014 | 1,428 |
26 | DAVID: Database for Annotation, Visualization, and Integrated Discovery | Genome Biology | 2003 | 1,411 |
27 | Expanded identification and characterization of mammalian circular RNAs | Genome Biology | 2014 | 1,361 |
28 | Ancient DNA and the rewriting of human history: be sparing with Occam’s razor | Genome Biology | 2016 | 1,335 |
29 | Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR | Genome Biology | 2016 | 1,334 |
30 | BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources | Genome Biology | 2009 | 1,216 |
31 | De novo assembly of bacterial transcriptomes from RNA-seq data | Genome Biology | 2015 | 1,215 |
32 | RNA virus interference via CRISPR/Cas13a system in plants | Genome Biology | 2018 | 1,148 |
33 | The plant microbiome | Genome Biology | 2013 | 1,028 |
34 | Chloroplast genomes: diversity, evolution, and applications in genetic engineering | Genome Biology | 2016 | 1,013 |
35 | The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community | Genome Biology | 2016 | 985 |
36 | Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies | Genome Biology | 2020 | 975 |
37 | HiGlass: web-based visual exploration and analysis of genome interaction maps | Genome Biology | 2018 | 950 |
38 | The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens | Genome Biology | 2019 | 938 |
39 | DNA methylation age of blood predicts all-cause mortality in later life | Genome Biology | 2015 | 928 |
40 | CIRI: an efficient and unbiased algorithm for de novo circular RNA identification | Genome Biology | 2015 | 921 |
41 | deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution | Genome Biology | 2016 | 917 |
42 | Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling | Genome Biology | 2016 | 912 |
43 | Pooling across cells to normalize single-cell RNA sequencing data with many zero counts | Genome Biology | 2016 | 912 |
44 | PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells | Genome Biology | 2019 | 911 |
45 | Circlator: automated circularization of genome assemblies using long sequencing reads | Genome Biology | 2015 | 910 |
46 | CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq | Genome Biology | 2016 | 900 |
47 | Transcriptome assembly from long-read RNA-seq alignments with StringTie2 | Genome Biology | 2019 | 897 |
48 | Cytoscape Automation: empowering workflow-based network analysis | Genome Biology | 2019 | 888 |
49 | Ten things you should know about transposable elements | Genome Biology | 2018 | 817 |
50 | The multidimensional mechanisms of long noncoding RNA function | Genome Biology | 2017 | 802 |