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3dfunc

ace-main

bacon

Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies

bacpi

A bi-directional attention neural network for compound–protein interaction and binding affinity prediction.

bayesimpute

a Bayesian imputation method for single-cell RNA-seq data

beprof

A comprehensive computational benchmark for evaluating deep learning-based protein function prediction approaches

bubble

A single-cell RNA-seq imputation method using an autoencoder constrained by bulk RNA-seq data

caco

cake

cellcircloc

CellCircLoc: Deep Neural Network for Predicting and Explaining Cell line-specific CircRNA Subcellular Localization

cgraphdta

A fusion-based deep learning architecture for detecting drug-target binding affinity using target sequence and structure

claire-release

comlmess

deepcelless

An interpretable deep learning-based cell line-specific essential protein predictior

deepdoguest

deepdtagen

deepep

a deep learning framework for essential protein prediction

deepfmb

Enhancing protein function prediction through the fusion of multi-type biological knowledge with protein language model and graph neural network

deepgoa

A deep learning framework for gene ontology annotation with sequence- and network-based information

deeplncloc

A deep learning-based lncRNA subcellular localization predictor

deepppf

deepppisp

Protein-protein interaction sites prediction through combining local and global features with deep neural networks

deepppisp-1

Protein-protein interaction sites prediction through combining local and global features with deep neural networks

dgp_hymm

HyMM: Hybrid method for disease-gene prediction by integrating multiscale module structures

dgp_nidm

dgp_prgefne

PrGeFNE: Predicting disease-related genes by fast network embedding

dmflda

A deep learning framework for predicting lncRNA–disease associations

dmflda2

dopcc

Detecting overlapping protein complexes via multi-metrics and co-core attachment method

dorc

Discovery of rare cells from ultra-large scRNA-seq data