其中results函数的解释:results extracts a result table from a DESeq analysis giving baseMeans across samples, log2foldchanges, standard errors, test statistics, p-values and adjusted p-values; resultsNames returns the names of the estimated effects (coefficents) of the model; removeResults returns...
Bulk2Space是一种基于深度学习框架的空间去卷积算法,该算法使用现有的高质量scRNA-seq数据和空间转录组学作为参考,从bulk RNA-seq中生成空间解析的单细胞表达谱。 Bulk2Space工作流程 Bulk2Space分为去卷积和空间映射两个步骤:首先在聚类空间内生成单细胞转录组数据,以找到一组细胞,其聚合数据与批量数据最接近。接下...
METAFlux可以根据bulk RNA-seq和scRNA-seq数据预测癌症代谢通量,以解决这些分析空白。METAFlux能够以nutrient-aware的方式使用癌症基因表达数据来表征整个代谢回路并输出non-degenerative通量。对于scRNA-seq 数据,METAFlux还检查TME中细胞类型之间的代谢异质性和相互作用。 METAFlux工作流程 METAFlux的性能测试 开发团队利用细胞...
今天给大家介绍的就是这篇发表在《Frontiers in Genetics》上题为"Integrated analysis of bulk and single-cell RNA sequencing reveals the interaction of PKP1 and tumor-infiltrating B cells and their therapeutic potential for nasopharyngeal carcinoma"的文章,IF=4.8。作者在文章的Acknowledgement也是对我们进行了...
进入CellPress官网后(https://www.cell.com/),我在部分期刊中对近5年基于RNA-seq的GSVA富集图进行了检索。 然后开启手动筛选模式,最后汇总出下面一张图: 可以看出,GSVA最终的呈现形式与分析差异基因的呈现形式类似,可以理解为分析差异基因集!可视化形式多样化,涉及热图、火山图、气泡图、条形图、柱状图等。
昨天老师发给我一篇生信女神Shirley Liu的文章,看了里面的内容之后感觉很兴奋~它可以不做免疫组测序,直接从Bulk RNA-seq或者scRNA-seq里面重构得到免疫组的信息。 中文翻译 文章要点 Although less sensitive than TCR-seq and BCR-seq, TRUST is able to identify the abundantly expressed and potentiallymore clona...
Fig. 4: Spatially resolved single-cell analysis of the mouse isocortex bulk data by Bulk2Space. aThe resources of the bulk transcriptome data, single-cell reference, and spatial reference. The bulk RNA-seq data of the mouse isocortex was sequenced using our in-house developed Spatial-seq whic...
Single cell and bulk RNA-seq data sources and processing Lung carcinoma tissue samples, sourced from the Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/), were analyzed for gene expression patterns. This analysis incorporated vital clinical factors like patient's survival status...
We present PyDESeq2, a python implementation of the DESeq2 workflow for differential expression analysis on bulk RNA-seq data. This implementation achieves better precision, allows speed improvements on large datasets, as shown in experiments on TCGA data, and can be more easily interfaced ...