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How to decode patient barcode inTCGA database ?

R tcga patient gdc written 2.6 years ago by Björn • 50 • updated 8 months ago by Biostar ♦♦ 20

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RNA-Seq database of cancer patients other than TCGA and ICGC?

patient rna-seq cancer written 2.1 years ago by thejustpark • 80 • updated 2.1 years ago by Pappu • 1.9k

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Recent Replies

C: Which normalization method/pipeline is best to generate normalized counts to mak by ATpoint ♦ 46k
Do the different datasets contain roughly the same celltypes or is this rather a mishmash of expe...
A: Loading a dataset via acession number by ATpoint ♦ 46k
This is RNA-seq, not microarrays which GEOquery assumes, so it is expected that it produces no ou...
C: NGS Data storage solutions for small organisations or big labs by A. Domingues • 2.4k
That was pretty much my low-tech solution, but I was just wondering of there was better way of go...
C: Extract column which contain <20 exons in a transcript by seidel ♦ 7.4k
Translation for us mortals :) Create a subprocess to count transcripts IDs (column 4), use awk to...
A: Search all SRA data for sequence? Raw reads only by Mensur Dlakic • 9.0k
Have you tried BLASTn from the NCBI web site? Simply select SRA as a target database from the dro...
A: How to change Rstudio language by ATpoint ♦ 46k
https://stackoverflow.com/questions/13575180/how-to-change-language-settings-in-r
C: How to average normalized counts of biological replicates by ATpoint ♦ 46k
Hello marina.rot! It appears that your post has been cross-posted to another site: https://suppo...
C: Recommendations for genome-wide genotyping platform, array and data analysis sof by GenoMax ♦ 96k
For example Illumina Omni arrays are between $200-$500 ([example LINK][1]). Large sequencing comp...
C: VEP is very slow. Fork doesnt seem to work by Collin • 870
Also, as it looks like you are trying to annotate somatic mutations (likely in cancer), OpenCRAVA...
C: VEP is very slow. Fork doesnt seem to work by Collin • 870
I'm not a VEP user, but if you can't figure it out then you can always use another variant annota...
A: Which normalization method/pipeline is best to generate normalized counts to mak by Mensur Dlakic • 9.0k
It seems like you want to normalize the data so that the number of transcripts in all datasets is...
A: determine the robustness of single-cell clusters by fracarb8 • 90
`scclusteval` (https://github.com/crazyhottommy/scclusteval) does exactly that.

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