CaRinDB: an integrated database of common cancer mutations and residue interaction network parameters [0.03%]
CaRinDB：一个关于常见癌症突变和残基相互作用网络参数的集成数据库
Daniela Coelho Batista Guedes Pereira,João Vitor Ferreira Cavalcante,Laise Florentino Cavalcanti et al.
Daniela Coelho Batista Guedes Pereira et al.
Motivation: Predicting the impact of missense mutations on protein structure and function is a fundamental challenge for cancer research and clinical applications. Despite all the computational advances and, more recently...
VST-DAVis: an R Shiny application and web-browser for spatial transcriptomics data analysis and visualization [0.03%]
VST-DAVis：一个用于空间转录组数据分析和可视化的R Shiny应用程序和网络浏览器
Sankarasubramanian Jagadesan,Chittibabu Guda
Sankarasubramanian Jagadesan
Summary: Visium HD Spatial Transcriptomics Data Analysis and Visualization (VST-DAVis) is an interactive, R Shiny application and web browser designed for intuitive analysis of spatial transcriptomics data generated using...
Shiny-Calorie: a context-aware application for indirect calorimetry data analysis and visualization using R [0.03%]
基于R的上下文感知间接量热数据计算与可视化应用软件(闪亮卡路里)
Stephan Grein,Tabea Elschner,Ronja Kardinal et al.
Stephan Grein et al.
Motivation: Indirect calorimetry is the standard method for metabolic phenotyping of animal models in pre-clinical research, supported by mature experimental protocols and widely used commercial platforms. However, a flex...
Pramesh Shakya,Ardalan Naseri,Degui Zhi et al.
Pramesh Shakya et al.
Motivation: The availability of large-scale genetic data presents a unique opportunity to study the genetic ancestries of individuals, which requires an efficient and scalable method. The existing global ancestry methods ...
Transcriptional and epigenetic regulation of Ca2+-signaling genes in hepatitis B-derived hepatocellular carcinoma and their association with the cancer hallmarks [0.03%]
乙型肝炎病毒导致的肝癌中钙信号通路基因的转录及表观遗传调控及其与肿瘤特征的关系研究
Guadalupe Hernández-Martínez,Andrés Hernández-Oliveras,Ángel Zarain-Herzberg et al.
Guadalupe Hernández-Martínez et al.
Motivation: Dysregulation of Ca2+-signaling genes has been shown in some types of cancer; however, it is virtually unknown in hepatitis B-derived hepatocellular carcinoma (HBV-HCC). Here, we evaluate the transcriptional a...
The nutrition toolbox permits in silico generation, analysis, and optimization of personalized diets through metabolic modelling [0.03%]
营养工具箱通过代谢建模实现个性化饮食的生成、分析和优化
Bram Nap,Bronson Weston,Annette Brandt et al.
Bram Nap et al.
Motivation: Nutrition is an important factor in human health, used to alleviate or prevent symptoms of various diseases. However, the effects of nutrition on the gut microbiome and human metabolism are not well understood...
Puzzler: scalable one-command platinum-quality genome assembly from HiFi and Hi-C [0.03%]
Puzzler：从HiFi和Hi-C进行高质量基因组组装的可扩展一键命令工具
Justin Merondun,Qingyi Yu
Justin Merondun
Motivation: Chromosome-level assemblies are essential for modern genomics, from comparative genomics and evolutionary studies to precision breeding. While integrated HiFi and Hi-C data now enable accurate chromosome-scale...
Adding highly variable genes to spatially variable genes can improve cell type clustering performance in spatial transcriptomics data [0.03%]
在空间转录组学数据中，将高度可变的基因添加到空间可变的基因中可以提高细胞类型聚类性能
Yijun Li,Stefan Stanojevic,Bing He et al.
Yijun Li et al.
Motivation: Spatial transcriptomics has allowed researchers to analyze transcriptome data in its tissue sample's spatial context. Various methods have been developed for detecting spatially variable genes (SV genes), whos...
Rosace-AA: enhancing interpretation of deep mutational scanning data with amino acid substitution and position-specific insights [0.03%]
Rosace-AA：利用氨基酸替代和位置特异性信息增强对深度突变扫描数据的解释
Jingyou Rao,Mingsen Wang,Matthew K Howard et al.
Jingyou Rao et al.
Motivation: Proteins are dynamic systems whose function and behavior are sensitive to environmental conditions and often involve multiple cellular roles. Deep mutational scanning (DMS) experiments generate extensive datas...
FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT) [0.03%]
从超字符串到索引：一种使用掩码Burrows-Wheeler变换(MBWT)的不受限制的k- mer集合的空间高效索引方法
Ondřej Sladký,Pavel Veselý,Karel Břinda
Ondřej Sladký
Motivation: The growing volumes and heterogeneity of genomic data call for scalable and versatile k-mer-set indexes. However, state-of-the-art indexes such as SBWT and SSHash depend on long non-branching paths in de Bruij...