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• TCGA Methylation Data CpG Islands
  I have been using Methylation data from TCGA, but not getting any clue of matching a record to re...
• Differentially methylated regions Analysis
  Hello All, I have TCGA data from RNAseq(Counts data) and DNA-Meth data. I am interested to condu...
• TCGA Methylation data is gone
  I was working with methylation data stored in TCGA couple months ago, but now the site changed an...
• TCGA methylation data format for COHCAP
  Hello, I want to use TCGA methylation data in COHCAP GUI to find DEM. But not able to understand,...
• How to transform DNA Methylation data in TCGA to effect of methylation on gene expression
  Hello everyone! DNA methylation data in TCGA describe the methylation extent of single site and...
• Batch correction for TCGA 450K data
  Hi, When working with Level 3 450K DNA methylation from TCGA, is there a batch correction and/or...
• Are There Any Alternatives To Methylkit For Methylation Call ?
  I have RRBS data. I tried to find differentially methylated promoter region using methylKit, but ...
• Methylation analysis with MEDIPS
  Hi, I have performed a differential methylation analysis using MEDIPS (R Bioconductor package) u...
• Clinical Survival data of TCGA
  I was wondering how  can I find out in the TCGA data   (has permission) that which patient has su...
• Tcga Illumina Methylation Combining 27K And 450K
  Hi everyone, There was a question on this long ago but no detailed answer was given to it, so I r...
• Doubts about TCGA DNA Methylation samples
  Hello everyone, I've tried to work with the TCGA DNA methylation data, but I'm having problems t...
• TCGA sample names for .idat files
  How can I map sample names (TCGA-XX-XXXX*) to .idat filenames for TCGA data? There must be a key ...
• TCGA data set with both expression (rna seq/ microarray) and exome seq of same samples?
  I have tried downloading some TCGA RNA seq data before from TCGA site, also trying TCGA-Assembler...
• Methylation and RNA seq data
  I am working on TCGA data for finding correlation between gene expression and methylation of a se...
• How to define and/or identify Partially methylated domain (DNA methylation)
  How to identify or define Partially methylated domains given processed DNA methylation data with ...
• Human Genome Germline Methylation Data
  Does anyone know if there is easily available germline methylation data for the human genome? pre...
• How To Get Gistic Or Rae Copy Number Variance Data Files For Copy Number Variance From Either Tcga Or Cbioportal?
  Does anyone have any idea how can get GISTIC or RAE data files for copy number variance from eith...
• CIMP markers in Infinium 450k Methylation Data (How To)
  I have methylation data for a group of patients done on the Infinium Methylation 450k platform. ...
• Working with Differentially Methylated Regions(DMRs)
  I was working on DNA methylation data downloaded from TCGA portal. Specifically I was working on ...
• Is there public (DNA methylation) data on circulating cell-free DNA - why not?
  In the near future, I will have to deal with circulating cell-free DNA in the context of finding ...
• TCGA COAD and READ annotations missing from GDC commons?
  I used to download data from the old TCGA annotations manager to identify DNU cases, but I could ...
• DNA methylation for certain region
  I would like to know your opinion on finding methylation from a data set of HumanMethylation450. ...
• Comparison of TCGA and SRA data
  Hello all, I am currently working on RNA seq analysis of TCGA and SRA cancer data.I have...
• Can DNA Methylation data of different samples from Human Methylation 27 and 450 platforms be combined using common set of 25,978 CpG sites?
  I am studying the Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) data set of TCGA. The DNA methyla...
• Best software to identify differentially methylated regions in Chipseq data?
  I'd like to hear opinions of those using chip seq methylation data. What is the best software to...