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tcgautils
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TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 17 months ago by
ATpoint
★ 4.1k • written 17 months ago by
Deniz
• 0
3
votes
4
replies
1.8k
views
Error with R package curatedTCGAData while trying to download TCGA MultiAssayExperiments
MultiAssayExperiment
curatedTCGAData
TCGAutils
3.4 years ago
svlachavas
▴ 830
3
votes
3
replies
1.2k
views
Error in MAE experiment regarding the replacement of internal assays with different number of features
MultiAssayExperiment
curatedTCGAData
TCGAutils
updated 3.4 years ago by
Marcel Ramos
690 • written 3.4 years ago by
svlachavas
▴ 830
3
votes
3
replies
1.3k
views
Implementation of MultiAssayExperiment and curatedTCGAData R packages for quering and prosessing multi-omics cancer datasets
MultiAssayExperiment
curatedTCGAData
TCGAutils
updated 3.4 years ago by
Marcel Ramos
690 • written 3.6 years ago by
svlachavas
▴ 830
5
votes
11
replies
3.9k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 4.8 years ago by
Marcel Ramos
690 • written 4.8 years ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
767
views
Breast cancer subtypes in TCGAutils
TCGAutils
updated 5.1 years ago by
Levi Waldron
★ 1.1k • written 5.1 years ago by
vittorio.fortino
• 0
3
votes
4
replies
1.3k
views
TCGAutils: Error in .checkBarcodes(barcodes) : barcode delimiters not consistent
TCGAutils
multiassayexperiment
coad
updated 5.9 years ago by
Marcel Ramos
690 • written 5.9 years ago by
mario.zanfardino
▴ 160
7 results • Page
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Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Votes
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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