SCpubr: a user-friendly R-package for generating publication-ready visualizations of single-cell transcriptome analyses [0.03%]
SCpubr：一个用户友好的R包，用于生成单细胞转录组分析的出版级可视化图表
Enrique Blanco-Carmona,Marcel Kool
Enrique Blanco-Carmona
Motivation: Single-cell RNA sequencing (scRNA-seq) is now a core technology for resolving cellular heterogeneity in complex samples, and standard analysis workflows produce a wide range of outputs, each requiring tailored...
EZ-Pair graph: scalable unified-axis visualization method for summarizing large-scale paired data [0.03%]
简易配对图：一种用于大规模配对数据概览的可扩展统一轴可视化方法
Akihiro Ezoe,Motoaki Seki,Keiichi Mochida
Akihiro Ezoe
Motivation: Avoiding dual-axis visualization improves quantitative interpretation. Yet for large-scale paired datasets, combining raw data with summary metrics on dual axes often hinders interpretability, while single-axi...
Differentially Expressed Gene Annotator (DEGAn): automated annotation and analysis of DEGs datasets with OS and PFS data [0.03%]
差异表达基因注释器（DEGAn）：带有OS和PFS数据的差异表达基因数据集的自动化注释与分析
Giuseppe Agapito,Mario Cannataro
Giuseppe Agapito
Motivation: High-throughput transcriptomic platforms routinely generate large differentially expressed gene (DEG) datasets, but linking these matrices to clinical outcomes still often requires manual data integration and ...
Fabio Bedin,Giorgia Cucina,Giampaolo Martinello et al.
Fabio Bedin et al.
Motivation: Proteomics has experienced substantial growth in methods and data analysis approaches, with the development of new data-dependent (DDA) and data-independent acquisition (DIA) workflow and several search engine...
Multi-Omic Bicluster Association Analysis (MOBAA)-a tool for identifying population subgroups with distinct multi-omics molecular profiles [0.03%]
多组学双聚类关联分析(MOBAA)-一种识别具有不同多组学分子特征的人群亚组的工具
Binisha H Mishra,Pashupati P Mishra
Binisha H Mishra
Motivation: The increasing availability of multi-omic datasets from the same individuals presents the opportunity to uncover distinct molecular profiles across subgroups within a study population. These profiles may be li...
CORTADO: hill climbing optimization for cell-type specific marker gene discovery and clustering accuracy improvement [0.03%]
一种用于细胞类型特异性标记基因发现和聚类准确度改进的爬山优化算法(Cortado)
Musaddiq K Lodi,Leiliani Clark,Satyaki Roy et al.
Musaddiq K Lodi et al.
Motivation: The advent of single-cell RNA sequencing (scRNA-seq) has enhanced our ability to study cellular heterogeneity. Accurately identifying distinct subpopulations and their defining markers is critical for understa...
K-FluDB: a novel K-mer-based database for enhanced genomic surveillance of Influenza A viruses [0.03%]
基于K-mer的新型流感病毒基因组监测数据库K-FluDB
Alejandro Uscanga Junco,Lorena Díaz-González,Blanca Taboada
Alejandro Uscanga Junco
Motivation: Influenza A viruses frequently cause seasonal outbreaks and pandemics due to their genetic diversity and reassortment potential. Existing genomic surveillance tools face challenges with redundant databases, de...
Kaminari: a frugal colored index for approximate k-mer queries [0.03%]
Kaminari：一种用于近似k-mer查询的简约着色索引
Victor Levallois,Yoshihiro Shibuya,Bertrand Le Gal et al.
Victor Levallois et al.
Motivation: Identifying which documents in a large database contain a query string is a fundamental problem in Information Retrieval and Computational Biology. We focus on the approximate version of this problem for genom...
MiRInter-Trans: a transformer-based framework for microRNA interaction prediction [0.03%]
基于Transformer的微小核糖核酸互作预测框架MiRInter-Trans
Marco Nicolini,Federico Stacchietti,Francisco Javier Molina et al.
Marco Nicolini et al.
Motivation: The accurate prediction of microRNA (miRNA) interactions represents a significant challenge in computational biology, with far-reaching implications for understanding gene regulatory networks and developing RN...
PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes [0.03%]
基于元基因组装配基因组的群体遗传分析的Nextflow管线PopMAG
Daniel Sabogal-Rodriguez,Alejandro Caro-Quintero
Daniel Sabogal-Rodriguez
Motivation: Metagenome-assembled genomes (MAGs) are routinely recovered from metagenomic studies, yet the population genetic information embedded within these datasets remains largely underutilized. Analyzing within-speci...