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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
3.4 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
1.2k
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 3.5 years ago by
svlachavas
▴ 830
5
votes
11
replies
3.8k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 4.8 years ago by
Marcel Ramos
690 • written 4.8 years ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
758
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: significant difference of p-values with dream() after updating VariancePartition
by
gabriel.hoffman
▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded
by
W. Evan Johnson
▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis
by
Alejandro Reyes
★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object
by
Alejandro Reyes
★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Answer: rlog transformation
by
Michael Love
41k
It is dependent on the other samples in the dataset.
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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