| ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees |
153 |
| iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data |
67 |
| Random forest versus logistic regression: a large-scale benchmark experiment |
53 |
| Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies |
50 |
| DrImpute: imputing dropout events in single cell RNA sequencing data |
43 |
| PseUI: Pseudouridine sites identification based on RNA sequence information |
42 |
| Rapid and precise alignment of raw reads against redundant databases with KMA |
38 |
| HH-suite3 for fast remote homology detection and deep protein annotation |
36 |
| Magic-BLAST, an accurate RNA-seq aligner for long and short reads |
27 |
| Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data |
27 |
| CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses |
23 |
| An interpretable framework for clustering single-cell RNA-Seq datasets |
22 |
| Web-based design and analysis tools for CRISPR base editing |
22 |
| Single sample scoring of molecular phenotypes |
19 |
| Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data |
19 |
| Deep convolutional neural networks for mammography: advances, challenges and applications |
18 |
| Assessing microscope image focus quality with deep learning |
18 |
| VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis |
18 |
| A network embedding-based multiple information integration method for the MiRNA-disease association prediction |
17 |
| HiCcompare: an R-package for joint normalization and comparison of HI-C datasets |
16 |
| How large B-factors can be in protein crystal structures |
16 |
| ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins |
16 |
| GOnet: a tool for interactive Gene Ontology analysis |
16 |
| Predicting drug-disease associations by using similarity constrained matrix factorization |
16 |
| A deep learning-based algorithm for 2-D cell segmentation in microscopy images |
16 |
| pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components |
16 |
| Predicting adverse drug reactions through interpretable deep learning framework |
15 |
| Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data |
15 |
| A new fruit fly optimization algorithm enhanced support vector machine for diagnosis of breast cancer based on high-level features |
15 |
| ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature |
15 |
| RnaSeqSampleSize: real data based sample size estimation for RNA sequencing |
15 |
| Predicting tumor cell line response to drug pairs with deep learning |
14 |
| Filtering procedures for untargeted LC-MS metabolomics data |
14 |
| SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data |
14 |
| Protein-protein interface hot spots prediction based on a hybrid feature selection strategy |
14 |
| Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data |
14 |
| Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi |
14 |
| Positive-unlabelled learning of glycosylation sites in the human proteome |
14 |
| Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0 |
14 |
| Oasis 2: improved online analysis of small RNA-seq data |
14 |
| Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples |
14 |
| UTAP: User-friendly Transcriptome Analysis Pipeline |
14 |
| Difficulty in inferring microbial community structure based on co-occurrence network approaches |
14 |
| DWNN-RLS: regularized least squares method for predicting circRNA-disease associations |
14 |
| SAMSA2: a standalone metatranscriptome analysis pipeline |
13 |
| FMLRC: Hybrid long read error correction using an FM-index |
13 |
| ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models |
13 |
| CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers |
13 |
| Deep learning models for bacteria taxonomic classification of metagenomic data |
12 |
| CollaboNet: collaboration of deep neural networks for biomedical named entity recognition |
12 |
