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TCGAutils
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TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 16 months ago by
ATpoint
★ 4.0k • written 16 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
3.3 years ago
svlachavas
▴ 830
3
votes
3
replies
1.1k
views
Error in MAE experiment regarding the replacement of internal assays with different number of features
MultiAssayExperiment
curatedTCGAData
TCGAutils
updated 3.3 years ago by
Marcel Ramos
690 • written 3.3 years ago by
svlachavas
▴ 830
3
votes
3
replies
1.2k
views
Implementation of MultiAssayExperiment and curatedTCGAData R packages for quering and prosessing multi-omics cancer datasets
MultiAssayExperiment
curatedTCGAData
TCGAutils
updated 3.3 years ago by
Marcel Ramos
690 • written 3.5 years ago by
svlachavas
▴ 830
5
votes
11
replies
3.8k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 4.7 years ago by
Marcel Ramos
690 • written 4.7 years ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
744
views
Breast cancer subtypes in TCGAutils
TCGAutils
updated 5.0 years ago by
Levi Waldron
★ 1.1k • written 5.0 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 5.8 years ago by
Marcel Ramos
690 • written 5.8 years ago by
mario.zanfardino
▴ 160
7 results • Page
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
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