单细胞数据虽然提高了信息挖掘的颗粒度,但是经常比较遗憾的是没有一些的临床信息(如治疗响应、耐药、复发信息等),因此scRNA-seq与bulk RNA-seq联合分析应运而生,既满足临床问题的研究可行性又对齐了颗粒度。 说到scRNA-seq与bulk RNA-seq数据的联合分析,就不得不提及到Scissor这个利器了,该软件于2021年发表在神刊...
单细胞数据虽然提高了信息挖掘的颗粒度,但是经常比较遗憾的是没有一些的临床信息(如治疗响应、耐药、复发信息等),因此scRNA-seq与bulk RNA-seq联合分析应运而生,既满足临床问题的研究可行性又对齐了颗粒度。 说到scRNA-seq与bulk RNA-seq数据的联合分析,就不得不提及到Scissor这个利器了,该软件于2021年发表在神刊...
批量RNA测序(bulk RNA-seq)可以在给定时间内揭示肿瘤中所有基因和TME的存在及数量,但如果没有细胞反卷积技术,仅凭总RNA表达量无法确定单个RNA分子的细胞起源。近期,科研人员开发了基于深度学习的反卷积方法,但这些方法往往需要对相同组织...
批量RNA测序(bulk RNA-seq)可以在给定时间内揭示肿瘤中所有基因和TME的存在及数量,但如果没有细胞反卷积技术,仅凭总RNA表达量无法确定单个RNA分子的细胞起源。近期,科研人员开发了基于深度学习的反卷积方法,但这些方法往往需要对相同组织类型的单细胞RNA-seq数据或配对流式细胞仪数据进行再训练,这限制了其临床应用。
由于可用的具有已知细胞组成的TME RNA-seq数据集十分有限,研究团队开发了组织和血液的人工RNA-seq,用于训练Kassandra算法,以稳健地识别不同的细胞群。所有可用的分类细胞群和癌症细胞系的组合被生成,以构建癌症特异性的人工转录组,模仿生物变异性。最终,共产生1800万和800万转录组,分别用于训练Kassandra-Tumor和Kassandra-...
Methods: In this study, we used blood whole transcriptome sequencing data (RNA-seq) from normal controls (Hlty) and patients with uncomplicated infection (Inf1 P), sepsis (Seps P), and septic shock (Shock P), to investigate the fraction changes of immune cell types...
Single-cell RNA-seq analysis Database, preprocessing and integration We processed a total of 32,261 cells sourced from the GEO database under accession number GSE155788, which were originated from two CCM3WTmice (controls) and two CCM3KOmice (CCM model). Cell capture and library preparation we...
We utilized the COPD bulk-seq dataset GSE76705 from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). In this dataset, the species analyzed wasHomo sapiens, and the assay platform used was GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. Peripheral blood mononu...
we predicted cell composition and observed significant differences between DCM and normal samples in fibroblasts, T cells, NK cells, and myeloid cells. Subsequently, we integrated two human single-cell RNA-seq datasets and conducted detailed analyses for these three cell types at the single-cell lev...
RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique for molecular profiling and immune characterization of tumors. In the past decade, many computational tools have been developed to characterize tumor immunity from gene expression data. However, the analysis of large-scale RNA...