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Analyze RPPA cancer data in R for clustering patients and differential protein expression

rppa de rppanalyzer clustering R written 3 months ago by svlachavas • 700

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218

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Calculating pathway activity from TCGA RPPA data

pathway R tcga rppa written 6 months ago by DBScan • 20 • updated 6 months ago by Kevin Blighe ♦ 71k

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1.6k

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Normalizing RPPA data counts from TCGA

tcga rppa protein expression written 2.2 years ago by vinayjrao • 200 • updated 2.2 years ago by Kevin Blighe ♦ 71k

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1.2k

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using limma for analyzing RPPA

rppa limma differential expression written 3.2 years ago by smt8n • 0

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902

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What can be learned from RPPA data?

rppa written 4.6 years ago by jzhou • 20

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Recent Replies

C: fineRADstructure file error by m.giakoumis1 • 0
I'm having this same issue! Did you ever figure out what the error means?
A: R org.Hs.eg.db matching ensembl gene ids with gene symbol by Kevin Blighe ♦ 71k
Another way: build a master table and use that: require(org.Hs.eg.db) keytypes(org.Hs.e...
C: Need help on installing poretools by dreamfeathers08 • 10
Hi Pierre, Thank you for your explanation. It helps in my understanding.
A: BLAST nr database by dxh0222 • 0
That means you open files limit is 256, you can change this limit with this code on terminal, uli...
C: find unique sequences among a set of fasta entries by GenoMax ♦ 96k
`kmercountexact.sh` from BBMap suite can also be used for this. What I am not sure of is how one...
C: find unique sequences among a set of fasta entries by Mensur Dlakic • 9.0k
This may help: - https://github.com/OpenGene/UniqueKMER
A: find unique sequences among a set of fasta entries by Mensur Dlakic • 9.0k
I suggest you try to count k-mers. Pick a decent size, say 31, and find all unique k-mers of that...
C: How do I effectively automate BLAST searches without using a local database? by Malcolm.Cook • 1.2k
- ho many snippets do you have? - how long is "forever"? - does each snippet take "forever"? - wh...
C: Version history and design files for exome kits from Agilent, Roche(Nimblegen), by GenoMax ♦ 96k
Are you sure? I click on file links and was asked to save the file for both links. I am not logge...
C: find unique sequences among a set of fasta entries by GenoMax ♦ 96k
Way you described would be the way to do it even if it seems inefficient. Since your sequences ar...
C: umi_tools using regex greedy quantifiers only returning 1 character by i.sudbery ♦ 11k
Hmmm.... Can you try it without the whitelist? UMI-tools will extract the barcodes first, and t...
A: Error in getBM: accessing Ensembl annotation with biomaRt by celia.escher • 10
res$ensembl <- gsub("\\..*","", res$ensembl) Perfectly worked!!! Many thanks! (instead ...

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