Clustering the data by similarity allows us to identify patterns within the features of interest. We are then able to summarize each pattern present in the data, rather than averaging across the entire feature
We next applied Spectra to scRNA-seq data from the challenging context of individuals with non-metastatic breast cancer before and after pembrolizumab (anti-PD-1) treatment (‘Bassez dataset’; Fig.2a)10. The original study used clustering and gene set analysis to identify therapy-induced changes...
标记基因(marker gene)的概念与差异表达(DE)基因的概念密切相关,但两个概念并不是不同义词。严格来说,标记基因选择是DE基因鉴定的一个子集,有效且有用的标记基因具有并非所有DE基因所共有的特定特征。广义上,我们将标记基因定义为可用于区分细胞亚群的基因。 文献标题及背景 A comparison of marker gene selection ...
While the coexpression network reflected globally coordinated cellular processes at the population level, the differential expression set revealed variability in subpopulation-specific gene expression. To further characterize this aspect, we looked at the clustering of the individual isolates based on expressi...
GECO (Gene Expression Clustering Optimization; theGECOapp.com) is a minimalistic GUI app that utilizes non-linear reduction techniques to rapidly visualize expression trends in many types of biological data matrices (such as bulk RNA-seq or proteomics).
tail = FALSE)) # determine overall cell clustering hc <- pagoda.cluster.cells(tam, varinfo) 代码语言:javascript 代码运行次数:0 运行 AI代码解释 # combine pathways that are driven by the same sets of genes: tamr <- pagoda.reduce.loading.redundancy(tam, pwpca, clpca) #combine aspects that...
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq
another in this weighted graph.Pis calculated fromS. The first K eigenvalues ofPare used to map the nodes of the graph to a K-dimensional space and the points in this reduced space can be grouped by any clustering algorithm. In this work, we have applied a hierarchical clustering algorithm...
Clustering is based on the results of phylogenetic analysis Zhou et al. BMC Plant Biology (2023) 23:429 Page 12 of 22 Fig. 2 (See legend on previous page.) Z hou et al. BMC Plant Biology (2023) 23:429 Page 13 of 22 Fig. 3 Cis-acting elements of...
predictions, we note that systematic errors during library preparation or in the assignment of amplicon reads to their pools of origin (for example, due to physical cross-contamination of library pools or index-switching of barcoded reads) could result in the false clustering of unrelated domain ...