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TCGABiolinks
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
7 weeks ago • updated 5 weeks ago
Giovanni Calice
▴ 160
1
vote
3
replies
3.0k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 5 weeks ago by
snijesh
▴ 20 • written 6.5 years ago by
Ramiro Magno
▴ 100
0
votes
1
reply
211
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 6 weeks ago by
BioinfoMug
• 0
1
vote
0
replies
155
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
8 weeks ago
BioinfoMug
• 0
0
votes
4
replies
972
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 9 weeks ago by
Marcel Ramos
690 • written 24 months ago by
Emre
• 0
0
votes
0
replies
153
views
GDC slides download
TCGAbiolinks
9 weeks ago
jain72744
• 0
0
votes
4
replies
273
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 10 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 10 weeks ago by
tirordep
• 0
0
votes
0
replies
143
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
11 weeks ago
Thalita
• 0
0
votes
1
reply
379
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
6 months ago
leon
• 0
0
votes
1
reply
608
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 8 months ago by
wrab425
• 0 • written 13 months ago by
snijesh
▴ 20
0
votes
0
replies
243
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical
TCGAbiolinks
9 months ago
BioInfoBeginnerrr
• 0
4
votes
8
replies
1.1k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago • updated 10 months ago
Habil Zare
▴ 200
0
votes
2
replies
846
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
12 months ago
qiz218591
• 0
13 results • Page
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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