catIN1_S1_L001_R1_001.fastqIN1_S1_L002_R1_001.fastq>IN1_S1_concatenated_R1_001.fastqcatIN1_S1_L001_R2_001.fastqIN1_S1_L002_R2_001.fastq>IN1_S1_concatenated_R2_001.fastqhttps://bioinformatics-core-shared-training.github.io/RNAseq-R/align-and-count.nb.htmllibrary(readr)library(dplyr)library(ggplot2)library(tidyverse)library(DESeq2)mycounts<-read.csv("C:/Users/?/Desktop/mycounts.csv&quo...[阅读全文]
longteng
随笔记录, 工作日记.
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(2024-11-22 19:09:54)
catIN1_S1_L001_R1_001.fastqIN1_S1_L002_R1_001.fastq>IN1_S1_concatenated_R1_001.fastqcatIN1_S1_L001_R2_001.fastqIN1_S1_L002_R2_001.fastq>IN1_S1_concatenated_R2_001.fastqhttps://bioinformatics-core-shared-training.github.io/RNAseq-R/align-and-count.nb.htmllibrary(readr)library(dplyr)library(ggplot2)library(tidyverse)library(DESeq2)mycounts<-read.csv("C:/Users/?/Desktop/mycounts.csv&quo...[阅读全文]
(2024-11-22 17:47:45)
https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.htmllibrary(TCGAbiolinks)library(maftools)getGDCprojects()query<-GDCquery(project="TCGA-HNSC",data.category="TranscriptomeProfiling",experimental.strategy='RNA-Seq',data.type="GeneExpressionQuantification",workflow.type="HTSeq-Counts")GDCdownload(query)d<-getResults(query)HNSC.Rna...[阅读全文]
(2024-03-23 15:45:30)
library(readr)library(dplyr)library(ggplot2)library(tidyverse)library(DESeq2)mycounts<-read.csv("C:/Users/~/Desktop/datacounts.csv")metadata<-read.csv("C:/Users/~/Desktop/datametadata.csv")countData<-mycounts[!(duplicated(mycounts[[1]])|duplicated(mycounts[[1]],fromLast=TRUE)),]rownames(mycounts)=make.names(mycounts$gene,unique=TRUE)mycounts<-as.data.frame(mycounts)...[阅读全文]
(2024-03-17 13:12:15)
library(dplyr)library(Seurat)library(patchwork)library(ggplot2)dat1<-Read10X("C:/Users/~/Desktop/data")#data(matrix.mtx.gz,barcode.tsv.gz,features.tsv.gz)dat1<-CreateSeuratObject(counts=dat1,project="NT",min.cells=3,min.features=200)dat1dat1[["percent.mt"]]<-PercentageFeatureSet(dat1,pattern="^MT-")VlnPlot(dat1,features=c("nFeature_RNA",&q...[阅读全文]
(2024-03-02 08:43:31)
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(2024-02-09 08:41:56)
library(Seurat)library(tibble)library(magrittr)library(patchwork)#Readindatadata<-data.table::fread("~/Downloads/~.txt.gz",data.table=F)#Genenamesareinthefirstcolumnsoweneedtomovethemtorownamesdata<-data%>%column_to_rownames("GENE")#CreateSeuratNT1<-CreateSeuratObject(counts=data,min.cells=3,min.features=350,project="NT1")data2<-data.table::fread("...[阅读全文]
