workflowrna-seqpipelinenextflowshinydeseq2microarraychip-seqatac-seqdifferential-expressionlimmagseanf-coredifferential-abundance UpdatedDec 18, 2024 Nextflow hbctraining/Intro-to-R-with-DGE Star59 workshopdeseq2rna-seq-datadge UpdatedMar 23, 2021 ...
We run ATAC samples that are not in distinct experimental groups (no replicates) but still would like to make a comparison between the number of reads of each sample in the consensus peaks. However, currently this is not possible because...
bin/bash## usage:Rscript run_deseq2.r ${name}.count.clean.txt $(name).deseq2.output.csv## args[i] 读入成字符串args=commandArgs(T)library(DESeq2)countdata<-read.table(paste("/public/home/xdyu/kcao/ChIP-seq-BWA-over/8.DESeq2/03.featurecount/",args[1],sep=""),header=TRUE,row...
前面说到DESeq2包需要准备两个输入文件,一个是样本列表矩阵,一个是row count定量表达矩阵,接下来我们要对样本进行两两比对,找到两组之间有多少个基因上调和下调,不进行两两比对直接把4组数据4个重复全部导进去得到的结果是没有意义的,这里用DESeq2做表达基因的差异分析 ...
Hi again, I am going through Documentation/results_description.html to understand which output I have. I do not find bwa/mergedLibrary/macs2/consensus/deseq2. Instead, I find bwa/mergedLibrary/macs/consensus and qc, i.e. no macs2 and no ...
since it reduces the time and resources of the analysis. One of the most used bioinformatics packages for the NGS analysis (including RNA-seq, ChIP-seq, ATAC-seq, Hi-C etc) is DESeq2(https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8). This package is part of ...