Showing : TCGAbiolinks • reset
2
votes
7
replies
231
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
updated 8 days ago by ▴ 250 • written 10 days ago by ▴ 170
0
votes
2
replies
214
views
RPPA data (Proteomics analysis)
TCGAbiolinks limma
8 weeks ago • updated 4 weeks ago qiz218591 • 0
1
vote
1
reply
153
views
Error when running getGDCprojects()
TCGAbiolinks
11 weeks ago DevelopingHippo • 0
0
votes
0
replies
125
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
12 weeks ago snijesh ▴ 20
0
votes
0
replies
98
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
12 weeks ago Manav • 0
1
vote
2
replies
355
views
Error when running GDC_prepare
TCGAbiolinks
3 months ago DevelopingHippo • 0
1
vote
3
replies
347
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
4 months ago Alexandre • 0
0
votes
0
replies
157
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
7 months ago lescano ▴ 10
0
votes
0
replies
221
views
Query on TCGA
TCGAbiolinks TCGAWorkflow
9 months ago hemangininaik09 • 0
0
votes
2
replies
612
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 9 months ago by ▴ 250 • written 11 months ago by • 0
0
votes
0
replies
324
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
10 months ago qiz218591 • 0
0
votes
0
replies
234
views
TCGAbiolinks file.type argument
TCGAbiolinks
10 months ago Elizabeth • 0
0
votes
0
replies
281
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
12 months ago syednajeebashraf • 0
5
votes
4
replies
1.8k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 12 months ago by ★ 1.2k • written 14 months ago by ▴ 30
0
votes
2
replies
469
views
GDCdownload Directory Problem :(
TCGAWorkflowData TCGAbiolinks
updated 9 months ago by 660 • written 13 months ago by • 0
0
votes
2
replies
1.4k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks TARGET-AML
updated 13 months ago by ▴ 250 • written 13 months ago by • 0
0
votes
1
reply
1.2k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 8 months ago by • 0 • written 13 months ago by • 0
3
votes
2
replies
1.6k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 13 months ago by • 0 • written 4.5 years ago by ▴ 10
2
votes
5
replies
992
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 13 months ago by • 0 • written 2.7 years ago by ▴ 40
0
votes
0
replies
296
views
GDCquery error when querying mutect2 data
TCGAbiolinks
14 months ago komal.rathi ▴ 110
0
votes
2
replies
1.4k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
14 months ago • updated 8 months ago spyrouglykeria • 0
6
votes
3
replies
2.3k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 13 months ago by • 0 • written 14 months ago by ▴ 10
2
votes
8
replies
3.5k
views
GDCquery_Maf error
TCGAbiolinks GDCquery_Maf
updated 10 months ago by • 0 • written 14 months ago by • 0
0
votes
0
replies
539
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
17 months ago constantinosdem • 0
0
votes
0
replies
405
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq TCGAbiolinks TCGAAnalyze_DEA
18 months ago Gandino • 0
0
votes
1
reply
1.4k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
19 months ago • updated 18 months ago raf4 ▴ 20
1
vote
2
replies
639
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
19 months ago raf4 ▴ 20
0
votes
1
reply
788
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 21 months ago by 40k • written 21 months ago by • 0
0
votes
0
replies
359
views
DEGs for legacy and harmonized dataset
#DEGs #legacydataset #harmonizeddataset TCGAbiolinks
updated 22 months ago by 3.8k • written 22 months ago by • 0
0
votes
1
reply
716
views
Help With TCGAbiolinks package
TCGAbiolinks data normalize l
updated 22 months ago by 3.8k • written 22 months ago by • 0
0
votes
2
replies
714
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
2.0 years ago H. Z. Amini • 0
0
votes
0
replies
1.1k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
2.0 years ago H. Z. Amini • 0
0
votes
0
replies
451
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
2.1 years ago rebeliscu • 0
0
votes
3
replies
596
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
2.1 years ago xiaofeiwang18266 ▴ 40
1
vote
1
reply
968
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 2.1 years ago by 40k • written 2.1 years ago by ▴ 40
3
votes
8
replies
2.7k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
2.2 years ago • updated 2.1 years ago xiaofeiwang18266 ▴ 40
0
votes
0
replies
543
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
2.2 years ago martin.schaefer • 0
0
votes
1
reply
511
views
library(TCGAbiolinks)
TCGAbiolinks
updated 2.3 years ago by 3.8k • written 2.3 years ago by • 0
0
votes
1
reply
891
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
2.4 years ago • updated 2.3 years ago Sophie Marion de Proce • 0
0
votes
1
reply
537
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 2.5 years ago by 3.5k • written 2.5 years ago by • 0
0
votes
5
replies
1.2k
views
TCGA: to extract clinical data from barcode
cancer TCGAbiolinks
updated 2.7 years ago by 3.8k • written 2.7 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 2.8 years ago by ▴ 260 • written 2.8 years ago by ▴ 40
4
votes
6
replies
1.1k
views
TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
2.8 years ago mario.zanfardino ▴ 160
0
votes
5
replies
1.0k
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks R.oo
updated 16 months ago by • 0 • written 2.9 years ago by ▴ 10
0
votes
2
replies
1.2k
views
TCGAbiolinks BioMart error
TCGAbiolinks BioMart
updated 2.9 years ago by 63k • written 2.9 years ago by ▴ 10
1
vote
3
replies
3.4k
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation permission denied RTCGAToolbox TCGAbiolinks
3.1 years ago julia.tutzauer • 0
0
votes
0
replies
646
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
3.4 years ago jam526 • 0
0
votes
1
reply
2.1k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
3.4 years ago ph.shimaasherif • 0
0
votes
0
replies
661
views
Error in downloading the MAF file for the TARGET data
TCGAbiolinks TARGET MAF
3.5 years ago ph.shimaasherif • 0
2
votes
4
replies
722
views
Error : Results must have the same dimensions
TCGAbiolinks GDC dataset
3.5 years ago ph.shimaasherif • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
Perhaps you are thinking of data analyses where the dependent variable is something other than expression itself. In the context of gene e…
Comment: Interpret plot from DiffBind by Chris • 0
If I want to find genes that are more open in diseased than control, I can filter out peaks that have highest log2Fold change like this, is…
Comment: Interpret plot from DiffBind by Chris • 0
Hi Rory. There are so many red dot above and below the blue line so it is hard to know which condition are more open, is that correct? Is 1…
Comment: Extract Limma Adjusted Values for Plotting by phelankj • 0
Thanks, on the normalized values using the same formula?
Answer: Extract Limma Adjusted Values for Plotting by James W. MacDonald 63k
You should use `removeBatchEffect` for that.
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
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