RNA-seq机制研究套餐采用了更高级的生信分析数据库Ingenuity Pathway Analysis(IPA)来对测序数据进行分析,IPA所基于的后台是一个高度结构化的ingenuity knowledge base数据库,并且它是一个收费数据库,每年的账号使用费数十万,该数据库经历20年的海量知识数据投入,号称拥有近500名PhD对近700多种权威杂志进行全文阅读,3000...
Pathway analysisRNA-seqStatistical geneticsA variety of pathway/gene-set approaches have been proposed to provide evidence of higher-level biological phenomena in the association of expression with experimental condition or clinical outcome. Among these approaches, it has been repeatedly shown that ...
Pathway analysis We’re going to use thegagepackage (Generally Applicable Gene-set Enrichment for Pathway Analysis) for pathway analysis. See also thegage package workflow vignette for RNA-seq pathway analysis. Once we have a list of enriched pathways, we’re going to us...
A principal component analysis (PCA) was performed using the function plotPCA in the DESeq2 R package to determine the interrelations between the individual samples using the normalized counts of all the genes after filtering as the input. The PCA plot shows a strong effect of the Parity Number...
利用Isoform view可以明确高通量RNAseq数据的生物学意义。利用功能蛋白结构域和异形体文献方面的信息,鉴定您实验中受到明显调控的异形体,并确定其潜在影响。 Gene and Chem View 利用IPA中的搜索功能,了解有关基因、药物、化学物质、蛋白质家族、正常细胞和疾病过程以及信号和代谢通路的最新发现。
et al. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Genome Biol 21, 36 (2020). https://doi.org/10.1186/s13059-020-1949-z 3. PROGENy安装及使用 3.1 安装 截止到本文发布前,PROGENy存储在Bioconductor的版本已经是最新的v1.20版本,和...
1,867 Commits .devcontainer Initial template commit May 15, 2024 .github updated changelog, added some more version bumps in docs and ci.yml Jul 22, 2024 assets Merge branch 'dev' ofhttps://github.com/qbic-pipelines/rnadeseqinto…
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没想到碰到了一个神器:PROGENy。可以给常见的14种signaling pathway活性打分。 参考:看着14个肿瘤相关通路活性就够了 buik RNA-seq: http://localhost:17435/notebooks/projects/cut_run/HDAC/RNA-seq.ipynb scRNA-seq: http://localhost:17435/notebooks/projects/ApcKO_multiomics/3.DEG_pathways.ipynb ...
GSVA分析的文章发表于2013年,GSVA: gene set variation analysis for microarray and RNA-Seq data 同样是broad 研究生出品,其在2005年PNAS发表的gsea已经高达1.4万的引用了,不过这个GSVA才不到300。去年我就介绍过一波它的分析流程,在:使用GSVA方法计算某基因集在各个样本的表现非常简单的代码,所以各个培训机构,公司...