Showing : tcgabiolinks • reset
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136
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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
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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 ▴ 20 • written 6.5 years ago by ▴ 100
0
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1
reply
210
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 6 weeks ago by • 0
1
vote
0
replies
154
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
8 weeks ago BioinfoMug • 0
0
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4
replies
970
views
GDCdownload Directory Problem :(
TCGAWorkflowData TCGAbiolinks
updated 9 weeks ago by 690 • written 24 months ago by • 0
0
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0
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152
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GDC slides download
TCGAbiolinks
9 weeks ago jain72744 • 0
0
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4
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272
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I need to calculate the survival rate of TCGA databases
TCGAbiolinks Survival
updated 10 weeks ago by ▴ 730 • written 10 weeks ago by • 0
0
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0
replies
143
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
11 weeks ago Thalita • 0
0
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1
reply
379
views
Problems when running GDC_prepare in R
TCGAbiolinks error GDC_prepare
6 months ago leon • 0
0
votes
1
reply
607
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 8 months ago by • 0 • written 13 months ago by ▴ 20
0
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0
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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
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2
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845
views
RPPA data (Proteomics analysis)
TCGAbiolinks limma
12 months ago qiz218591 • 0
1
vote
1
reply
753
views
Error when running getGDCprojects()
TCGAbiolinks
13 months ago DevelopingHippo • 0
0
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0
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534
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
13 months ago Manav • 0
1
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2
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1.5k
views
Error when running GDC_prepare
TCGAbiolinks
14 months ago DevelopingHippo • 0
1
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3
replies
926
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
15 months ago Alexandre • 0
0
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0
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455
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
18 months ago lescano ▴ 10
0
votes
2
replies
2.1k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
2.0 years ago • updated 18 months ago spyrouglykeria • 0
0
votes
1
reply
1.9k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 19 months ago by • 0 • written 2.0 years ago by • 0
0
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0
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628
views
Query on TCGA
TCGAbiolinks TCGAWorkflow
19 months ago hemangininaik09 • 0
0
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2
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1.3k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 20 months ago by ▴ 270 • written 22 months ago by • 0
2
votes
8
replies
4.8k
views
GDCquery_Maf error
TCGAbiolinks GDCquery_Maf
updated 21 months ago by • 0 • written 2.1 years ago by • 0
0
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0
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716
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
21 months ago qiz218591 • 0
0
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0
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516
views
TCGAbiolinks file.type argument
TCGAbiolinks
21 months ago Elizabeth • 0
0
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0
replies
535
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
23 months ago syednajeebashraf • 0
5
votes
4
replies
2.8k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 23 months ago by ★ 1.3k • written 2.1 years ago by ▴ 30
0
votes
2
replies
2.1k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks TARGET-AML
updated 24 months ago by ▴ 270 • written 2.0 years ago by • 0
2
votes
5
replies
1.5k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 2.0 years ago by • 0 • written 3.6 years ago by ▴ 40
3
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2
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2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.0 years ago by • 0 • written 5.4 years ago by ▴ 10
6
votes
3
replies
3.1k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.0 years ago by • 0 • written 2.1 years ago by ▴ 10
0
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0
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563
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.0 years ago komal.rathi ▴ 120
0
votes
5
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1.5k
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks R.oo
updated 2.3 years ago by • 0 • written 3.8 years ago by ▴ 10
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0
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798
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.4 years ago constantinosdem • 0
0
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0
replies
666
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq TCGAbiolinks TCGAAnalyze_DEA
2.4 years ago Gandino • 0
0
votes
1
reply
2.1k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
2.5 years ago raf4 ▴ 20
1
vote
2
replies
1.0k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
2.5 years ago raf4 ▴ 20
0
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1
reply
1.3k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
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0
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704
views
DEGs for legacy and harmonized dataset
#DEGs #legacydataset #harmonizeddataset TCGAbiolinks
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
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1
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1.1k
views
Help With TCGAbiolinks package
TCGAbiolinks data normalize l
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
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2
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1.1k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
2.9 years ago H. Z. Amini ▴ 10
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0
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1.6k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
2.9 years ago H. Z. Amini ▴ 10
0
votes
3
replies
4.3k
views
Problem in downloading data via TCGAbiolinks
tcgabiolinks tcgadownload
updated 2.9 years ago by ▴ 10 • written 7.8 years ago by ▴ 10
0
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0
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721
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
2.9 years ago rebeliscu • 0
0
votes
3
replies
925
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
3.0 years ago xiaofeiwang18266 ▴ 50
1
vote
1
reply
1.3k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 3.0 years ago by 41k • written 3.0 years ago by ▴ 50
3
votes
8
replies
3.5k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
3.1 years ago • updated 3.0 years ago xiaofeiwang18266 ▴ 50
0
votes
1
reply
765
views
error reading from connection
TCGAbiolinks
updated 3.1 years ago by ★ 3.9k • written 4.5 years ago by • 0
0
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0
replies
843
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
3.1 years ago martin.schaefer • 0
0
votes
1
reply
1.7k
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
3.3 years ago • updated 3.2 years ago Sophie Marion de Proce • 0
50 results • Page 1 of 1
Recent ...
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Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Votes
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?
Answer: How to retrieve gene ontology GO class from gene list?
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