Intron retention analysis was performed on BRCA TCGA RNA sequencing datasets (Koboldt et al., 2012). TCGA fastq reads were mapped using the STAR aligner (v2.3.1) (Dobin et al., 2013) onto the hg19/GRCh37 reference genome as previously described (Hsu et al., 2015). Level of intron ...
## [1] parallel stats4 stats graphics grDevices utils datasets ## [8] methods base ## ## other attached packages: ## [1] tictoc_1.0.1 jsonlite_1.8.0 ## [3] vroom_1.5.7 forcats_0.5.1 ## [5] stringr_1.4.0 dplyr_1.0.9 ## [7] purrr_0.3.4 readr_2.1.2 ## [9] tidyr_1...
We describe here a suite of algorithms and tools implemented in the MAJIQ v2 package to address challenges in detection, quantification, and visualization of splicing variations from such datasets. Using both large scale synthetic data and GTEx v8 as benchmark datasets, we assess the advantages of...
函数".libPaths()"能够显示库所在的位置,函数"library()"则可以显示库中有哪些包。其中R中自带了一系列默认包(包括base、datasets、utils、grDevices、graphics、stats以及methods),它们提供了种类繁多的默认函数和数据集。而其他包则需要通过下载来进行安装,安装好后必须被载入才能使用。第一次安装一个包,需要选择CRAN...
## Publicly available datasets usually have the read length in the description. Sometimes they are called the number of cycles. simpleaf index \ -o simpleaf_index \ -f toy_human_ref/fasta/genome.fa \ -g toy_human_ref/genes/genes.gtf \ ...
GEO:Submit RNA-seq, ChIP-seq, and other types of gene expression and epigenomics datasets. 也就是我们常用的基因表达数据,这里可以上传处理后的数据,如count和TPM,FPKM等 BioProject & BioSample:这是NCBI的核心组织架构,一篇文章就是一个BioProject,一个project里可以包含多个BioSample ...
Integrated analysis of a compendium of RNA-Seq datasets for splicing factors Article Open access 16 June 2020 rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data Article 23 February 2024 NBBt-test: a versatile method for dif...
RNA CoMPASS leverages existing tools and parallel computing technology to facilitate the analysis of even very large datasets. RNA CoMPASS has a web-based graphical user interface with intrinsic queuing to control a distributed computational pipeline. RNA CoMPASS was evaluated by analyzing RNA-seq data...
data=listDatasets(mart)data2=useDataset("hsapiens_gene_ensembl",mart=mart) 可在data2中生成智人ensembl的基因组。 下面开始转换。导入数据 (导入数据前记得在原csv文件的A1中加入列名“Gene_ID”,后续代码有利用到,而源文件没有这个列名): RNA_seq<-read_csv("GSE213001_Entrez-IDs-Lung-IPF-GRCh38-p12-...
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the join