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Analysing high-throughput sequencing data in Python with HTSeq 2.0

Bioinformatics, 2022-05, Vol.38 (10), p.2943-2945

2022

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SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

Bioinformatics, 2022-05, Vol.38 (11), p.3128-3131

2022

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GNN-based embedding for clustering scRNA-seq data

Bioinformatics, 2022-01, Vol.38 (4), p.1037-1044

2022

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Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data

Bioinformatics (Oxford, England), 2022-09, Vol.38 (19), p.4522-4529

2022

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DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing

Bioinformatics, 2022-05, Vol.38 (11), p.3113-3115

2022

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monaLisa: an R/Bioconductor package for identifying regulatory motifs

Bioinformatics (Oxford, England), 2022-04, Vol.38 (9), p.2624-2625

2022

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CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks

Bioinformatics (Oxford, England), 2022-02, Vol.38 (5), p.1277-1286

2022

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LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism

Bioinformatics (Oxford, England), 2023-12, Vol.39 (12)

2023

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XGBLC: an improved survival prediction model based on XGBoost

Bioinformatics, 2022-01, Vol.38 (2), p.410-418

2022

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E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants

Bioinformatics (Oxford, England), 2022-11, Vol.38 (23), p.5168-5174

2022

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A convolutional neural network and graph convolutional network-based method for predicting the classification of anatomical therapeutic chemicals

Bioinformatics (Oxford, England), 2021-09, Vol.37 (18), p.2841-2847

2021

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MARSY: a multitask deep-learning framework for prediction of drug combination synergy scores

Bioinformatics (Oxford, England), 2023-04, Vol.39 (4)

2023

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Polyaniline: Synthesis, properties, and application

Polymer science. Series C, 2014-09, Vol.56 (1), p.144-153

2014

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WMSA: a novel method for multiple sequence alignment of DNA sequences

Bioinformatics (Oxford, England), 2022-11, Vol.38 (22), p.5019-5025

2022

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LanceOtron: a deep learning peak caller for genome sequencing experiments

Bioinformatics, 2022-09, Vol.38 (18), p.4255-4263

2022

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EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning

Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)

2023

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blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation

Bioinformatics, 2022-04, Vol.38 (8), p.2356-2357

2022

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Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning

Bioinformatics (Oxford, England), 2023-06, Vol.39 (6)

2023

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scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data

Bioinformatics (Oxford, England), 2024-02, Vol.40 (2)

2024

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cellCounts: an R function for quantifying 10x Chromium single-cell RNA sequencing data

Bioinformatics (Oxford, England), 2023-07, Vol.39 (7)

2023

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The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data

Bioinformatics (Oxford, England), 2023-02, Vol.39 (2)

2023

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nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis

Bioinformatics (Oxford, England), 2024-01, Vol.40 (1)

2024

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HGC: fast hierarchical clustering for large-scale single-cell data

Bioinformatics (Oxford, England), 2021-11, Vol.37 (21), p.3964-3965

2021

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Inference of 3D genome architecture by modeling overdispersion of Hi-C data

Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)

2023

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DeepMicroGen: a generative adversarial network-based method for longitudinal microbiome data imputation

Bioinformatics (Oxford, England), 2023-05, Vol.39 (5)

2023

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Analysing high-throughput sequencing data in Python with HTSeq 2.0

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

GNN-based embedding for clustering scRNA-seq data

Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data

DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing

monaLisa: an R/Bioconductor package for identifying regulatory motifs

CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks

LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism

XGBLC: an improved survival prediction model based on XGBoost

E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants

A convolutional neural network and graph convolutional network-based method for predicting the classification of anatomical therapeutic chemicals

MARSY: a multitask deep-learning framework for prediction of drug combination synergy scores

Polyaniline: Synthesis, properties, and application

WMSA: a novel method for multiple sequence alignment of DNA sequences

LanceOtron: a deep learning peak caller for genome sequencing experiments

EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning

blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation

Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning

scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data

cellCounts: an R function for quantifying 10x Chromium single-cell RNA sequencing data

The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data

nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis

HGC: fast hierarchical clustering for large-scale single-cell data

Inference of 3D genome architecture by modeling overdispersion of Hi-C data

DeepMicroGen: a generative adversarial network-based method for longitudinal microbiome data imputation

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