TCGA CIMP status

How can I assign CIMP status to the patients of my cohort from TCGA-COAD? Are there any R packages available to do so with the RNA-seq expression data or the methylation data?

coad tcga

• 583 views • link

updated 3.7 years ago by Ram

• written 4.1 years ago by ilomilo •

0 answers

No answers yet.

More posts like this

Clinical cohort for cancer sequenced using scRNA-Seq
written 3.1 years ago by Nitin Narwade

Just curious about the availability of single-cell RNA-Seq data with clinical attributes. All the transcriptomic data I found for the patients which have clinical parameters …
Download Isoform expression data from tcga
written 3.8 years ago by nourmahfel •

I am trying to identify the isoform of a gene that is overexpressed in cancer samples versus normal. Is there packages that would allow me …
duplicate values/samples TCGA
written 4.5 years ago by Rob •

For the deseq2 differential gene expression analysis, I have TCGA patients. Some of them are duplicates. How can I remove my duplicate patients? which one …
Differential expression analysis for genes in different stages of cancer by TCGA clinical data
written 4.6 years ago by Zahra •

Hi all, I want to perform differential expression analysis for some genes in different stages of cancer by TCGA RNA-Seq data. I use the TCGA …
Correlation between gene expression (RNAseq) and RRBS methylation data
written 6.4 years ago by rahel14350 •

Dear all, I have data from gene expression (RNAseq) and RRBS methylation data from mm10. I would like to calculate the Correlation between this data. …
CIMP markers in Infinium 450k Methylation Data (How To)
written 9.8 years ago by gaiusjaugustus

I have methylation data for a group of patients done on the Infinium Methylation 450k platform. I want to look at the samples and determine …
ALL RNA-seq publicly available data
written 11.5 years ago by a.james

Hello All, I need to do a correlation study with publicly available ALL RNA-seq data samples with in house RNA-seq sample (a single patient sample …
Bioconductor packages for comparing different species data (particularly RNA-seq and DNA methylatio…
written 11.9 years ago by Saad Khan

Are there any available bioconductor packages for comparing RNA-seq and/or DNA methylation data within two species?
Microarray | RNA Seq | Methylation Arrays - Correlations?
written 12.3 years ago by andrew.j.skelton73

Hi, I've compared RNA Seq data to Microarray data (Downstream - same tissue cohort), by taking Mean expression of genes in the microarray and comparing …
Scaling Rpkm/Fpkm Values Between 0 And 1
written 12.6 years ago by skm770 •

<p>Rpkm and fpkm values vary a lot some times from 10^-6 to 10^6. I have seen people comparing methylation with RNA-seq. Since methylation usually lies …