Rafael Castelli,Tomás González,Rodrigo Torrado et al.
Rafael Castelli et al.
Motivation: Efficient data compression is crucial for reducing storage and transmission costs associated to vast volumes of nanopore raw sequencing data. Surpassing the state-of-the-art compression performance has been ch...
Impact of sequencing read quality on whole-genome sequencing outcomes for foodborne pathogens using a BacWORK standardized analysis workflow [0.03%]
测序读段质量对食品中病原体BacWORK标准化分析工作流程的全基因组测序结果的影响
Arnaud Felten,Deborah Merda,Meryl Vila Nova et al.
Arnaud Felten et al.
Motivation: Whole-genome sequencing (WGS) is now routinely used for surveillance and outbreak investigations of foodborne pathogens. However, the reliability of downstream analyses strongly depends on sequencing read qual...
metaAPA: a tool for integration of PolyA site predictions from single-cell and spatial transcriptomics [0.03%]
metaAPA：一个用于整合来自单细胞和空间转录组学的PolyA位点预测的工具
Qian Zhao,Magnus Rattray
Qian Zhao
Motivation: Single-cell 3'-tagging sequencing, such as that provided by 10x Genomics, can be used to study alternative polyadenylation (APA). APA can affect RNA function, stability, and subcellular localization, thereby i...
TransPilot: mining key transcription factors by correlating binding sites with differentially expressed genes [0.03%]
基于转录因子结合位点与差异表达基因相关性的关键转录因子挖掘算法研究
Huang Tinghua,Yao Min,Zhang Fanghong et al.
Huang Tinghua et al.
Motivation: Current software packages to mine key transcription factors (TFs) regulating the differentially expressed genes (DEGs) have not been satisfactorily utilized. ...
Pylluminator: fast and scalable analysis of DNA methylation data in Python [0.03%]
Pylluminator：Python中快速且可扩展的DNA甲基化数据分析工具
Elio Fanchon,Benjamin Loire,Jean-Philippe Trani et al.
Elio Fanchon et al.
Motivation: Illumina Infinium BeadChip technology for DNA methylation analysis continues to expand, with the latest EPICv2 arrays targeting about a million loci. As data volumes from this technology continue to grow, ther...
Structome-TM: complementing dataset assembly for structural phylogenetics by addressing size-based biases [0.03%]
结构组学-TM：通过解决基于大小的偏差来完善数据集装配以进行结构系统发生学研究
Ashar J Malik,David B Ascher
Ashar J Malik
Motivation: Harnessing the explosion of protein structure data to uncover deep evolutionary relationships requires effective comparison methods. While widely used global alignment techniques are powerful, they can fail to...
eMZed 3: flexible and interactive development of scalable LC-MS/MS data analysis workflows in python [0.03%]
eMZed 3：python中灵活交互式的开发可扩展LC-MS/MS数据分析工作流
Uwe Schmitt,Jethro Hemmann,Nicola Zamboni et al.
Uwe Schmitt et al.
Summary: Liquid chromatography-mass spectrometry (LC-MS/MS) data analysis requires adaptable software solutions to meet diverse analytical needs. We present eMZed 3, a modern Python framework for flexible and interactive ...
Riasat Azim,Sabab Aosaf,Swakkhar Shatabda et al.
Riasat Azim et al.
Summary: Spatial transcriptomics (ST) enables high-resolution exploration of tissue architecture by integrating gene expression profiles with spatial information, thereby advancing insights into cellular composition, orga...
Identification of monotonically classifying pairs of genes for ordinal disease outcomes [0.03%]
识别有序疾病结局的单调分类基因对
Océane Fourquet,Daria Afenteva,Kaiyang Zhang et al.
Océane Fourquet et al.
Summary: We extend an existing classification method for identifying pairs of genes whose joint expression is associated with binary outcomes to ordinal multi-class outcomes, such as overall survival or disease progressio...
A fusion-based multiomics classification approach for enhanced gene discovery in non-small cell lung cancer [0.03%]
一种融合的多组学分类方法，可增强非小细胞肺癌中的基因发现
Kountay Dwivedi,Amirreza Mahbod,Rupert C Ecker et al.
Kountay Dwivedi et al.
Motivation: This study introduces a fusion-based multiomics approach to identifying non-small cell lung cancer (NSCLC)-relevant genes. We evaluated the NSCLC-subtype classification performance of various state-of-the-art ...