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tcgautils
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TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 2.1 years ago by
ATpoint
★ 4.6k • written 2.1 years ago by
Deniz
• 0
3
votes
4
replies
2.2k
views
Error with R package curatedTCGAData while trying to download TCGA MultiAssayExperiments
MultiAssayExperiment
curatedTCGAData
TCGAutils
4.0 years ago
svlachavas
▴ 840
3
votes
3
replies
1.4k
views
Error in MAE experiment regarding the replacement of internal assays with different number of features
MultiAssayExperiment
curatedTCGAData
TCGAutils
updated 4.1 years ago by
Marcel Ramos
700 • written 4.1 years ago by
svlachavas
▴ 840
3
votes
3
replies
1.5k
views
Implementation of MultiAssayExperiment and curatedTCGAData R packages for quering and prosessing multi-omics cancer datasets
MultiAssayExperiment
curatedTCGAData
TCGAutils
updated 4.1 years ago by
Marcel Ramos
700 • written 4.2 years ago by
svlachavas
▴ 840
5
votes
11
replies
4.6k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 5.4 years ago by
Marcel Ramos
700 • written 5.4 years ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
898
views
Breast cancer subtypes in TCGAutils
TCGAutils
updated 5.7 years ago by
Levi Waldron
★ 1.1k • written 5.7 years ago by
vittorio.fortino
• 0
3
votes
4
replies
1.6k
views
TCGAutils: Error in .checkBarcodes(barcodes) : barcode delimiters not consistent
TCGAutils
multiassayexperiment
coad
updated 6.5 years ago by
Marcel Ramos
700 • written 6.5 years ago by
mario.zanfardino
▴ 160
7 results • Page
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Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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