### 读入下载的数据 tcga_count <- read_tsv(file = './TCGA-LUAD.htseq_counts.tsv.gz') # count数据 tcga_fpkm <- read_tsv(file = "./TCGA-LUAD.htseq_fpkm.tsv.gz") # fpkm数据 tcga_survival <- read_tsv(file = "./TCGA-LUAD.survival.tsv") # 患者生存状态 tcga_phenotype <- rea...
https://gdc.xenahubs.net/download/TCGA-LAML/Xena_Matrices/TCGA-LAML.htseq_counts.tsv.gz https://gdc.xenahubs.net/download/TCGA-ACC/Xena_Matrices/TCGA-ACC.htseq_counts.tsv.gz 绝大部分文件的下载地址中,网址的规律是: https://gdc.xenahubs.net/download/TCGA-疾病名称/Xena_Matrices/TCGA-疾病...
https://gdc.xenahubs.net/download/TCGA-LAML/Xena_Matrices/TCGA-LAML.htseq_counts.tsv.gzhttps://gdc.xenahubs.net/download/TCGA-ACC/Xena_Matrices/TCGA-ACC.htseq_counts.tsv.gz 绝大部分文件的下载地址中,网址的规律是: 代码语言:javascript 代码运行次数:0 运行 AI代码解释 https://gdc.xenahubs.n...
1.https://gdc.xenahubs.net/download/TCGA-LAML/Xena_Matrices/TCGA-LAML.htseq_counts.tsv.gz 2.https://gdc.xenahubs.net/download/TCGA-ACC/Xena_Matrices/TCGA-ACC.htseq_counts.tsv.gz 3.https://gdc.xenahubs.net/download/TCGA-LAML/Xena_Matrices/TCGA-LAML.survival.tsv.gz 4.https://gdc....
RNA-seq表达矩阵:TCGA-BRCA.htseq_counts.tsv 临床数据:TCGA-BRCA.GDC_phenotype.tsv 突变数据:TCGA.BRCA.mutect.maf.gz AI代码助手复制代码 1.2 数据清洗 去除低表达基因(TPM/FPKM < 1的基因在>50%样本中表达) 标准化处理(推荐DESeq2的vst转换或log2(TPM+1)) ...
[7] "TCGA-LUAD.htseq_counts.tsv" "TCGA-STAD.htseq_counts.tsv" # [9] "TCGA-TGCT.htseq_counts.tsv" "TCGA-UVM.htseq_counts.tsv" # [11] "TCGA-PAAD.htseq_counts.tsv" "TCGA-GBM.htseq_counts.tsv" # [13] "TCGA-COAD.htseq_counts.tsv" "TARGET-NBL.htseq_counts.tsv" # [15]...
https://gdc.xenahubs.net/download/TCGA-ACC/Xena_Matrices/TCGA-ACC.htseq_counts.tsv.gz https://gdc.xenahubs.net/download/TCGA-LAML/Xena_Matrices/TCGA-LAML.survival.tsv.gz https://gdc.xenahubs.net/download/TCGA-ACC/Xena_Matrices/TCGA-ACC.GDC_phenotype.tsv.gz ...
1、像上述XENA直接下载下来的注释文件(gencode.v22.annotation.gene.probeMap)跟同一网页下载下来的表达矩阵文件(TCGA-LUAD.htseq_fpkm.tsv.gz或者TCGA-LUAD.htseq_counts.tsv.gz),其实他们的Ensembl_ID是完全一样的,这样其实可以不用拆解Ensembl_ID的小数点,直接提取protein_coding并将表达矩阵的Ensembl_ID匹配到...
["TCGA-LUAD"]}},#{#"op":"in",#"content":{#"field":"cases.demographic.gender",#"value":["female"]#}#},{"op":"in","content":{"field":"files.analysis.workflow_type","value":["HTSeq - Counts"]}}]}pre='''{"filters":{"op":"in","content":{"field":"files.submitter_id...
看规律 1. https://gdc.xenahubs.net/download/TCGALAML/Xena_Matrices/TCGA-LAML.htseq_counts.tsv.gz 2. https://gdc.xenahubs.net/download/TCGAACC/Xena_Matrices/TCGA-ACC.htseq_counts.tsv.gz 3. https://gdc.xenahubs.net/download/TCGALAML/Xena_Matrices/TCGA-LAML.survival.tsv.gz 4. https...