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tcgabiolinks
•
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0
votes
1
reply
215
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
0
votes
0
replies
139
views
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
0
replies
158
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
0
replies
156
views
GDC slides download
TCGAbiolinks
10 weeks ago
jain72744
• 0
0
votes
4
replies
279
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
145
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
12 weeks ago
Thalita
• 0
0
votes
1
reply
385
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
6 months ago
leon
• 0
0
votes
0
replies
245
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical
TCGAbiolinks
9 months ago
BioInfoBeginnerrr
• 0
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago • updated 10 months ago
Habil Zare
▴ 200
0
votes
2
replies
849
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
13 months ago • updated 12 months ago
qiz218591
• 0
1
vote
1
reply
757
views
Error when running getGDCprojects()
TCGAbiolinks
13 months ago
DevelopingHippo
• 0
0
votes
1
reply
614
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
539
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
13 months ago
Manav
• 0
1
vote
2
replies
1.5k
views
Error when running GDC_prepare
TCGAbiolinks
14 months ago
DevelopingHippo
• 0
1
vote
3
replies
936
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
15 months ago
Alexandre
• 0
0
votes
0
replies
459
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
18 months ago
lescano
▴ 10
0
votes
0
replies
634
views
Query on TCGA
TCGAbiolinks
TCGAWorkflow
20 months ago
hemangininaik09
• 0
0
votes
0
replies
719
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
21 months ago
qiz218591
• 0
0
votes
0
replies
518
views
TCGAbiolinks file.type argument
TCGAbiolinks
21 months ago
Elizabeth
• 0
0
votes
2
replies
1.3k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
updated 20 months ago by
Tiago C. Silva
▴ 270 • written 22 months ago by
JAcky
• 0
0
votes
0
replies
537
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks
TCGAbiolinksGUI.data
SummarizedExperiment
23 months ago
syednajeebashraf
• 0
0
votes
4
replies
980
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 9 weeks ago by
Marcel Ramos
690 • written 24 months ago by
Emre
• 0
0
votes
1
reply
1.9k
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 19 months ago by
Aurora
• 0 • written 2.0 years ago by
mahsa
• 0
0
votes
2
replies
2.1k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks
TARGET-AML
updated 2.0 years ago by
Tiago C. Silva
▴ 270 • written 2.0 years ago by
Лиза
• 0
0
votes
0
replies
568
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.0 years ago
komal.rathi
▴ 120
0
votes
2
replies
2.1k
views
GDCprepare() - R Session Aborted
TCGAbiolinks
R
GDCprepare()
2.0 years ago • updated 18 months ago
spyrouglykeria
• 0
6
votes
3
replies
3.1k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.0 years ago by
Nikolas
• 0 • written 2.1 years ago by
lescano
▴ 10
5
votes
4
replies
2.8k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 23 months ago by
swbarnes2
★ 1.3k • written 2.1 years ago by
vm
▴ 30
2
votes
8
replies
4.8k
views
GDCquery_Maf error
TCGAbiolinks
GDCquery_Maf
updated 21 months ago by
1526466763
• 0 • written 2.1 years ago by
e.iich
• 0
0
votes
0
replies
801
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.4 years ago
constantinosdem
• 0
0
votes
0
replies
668
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
votes
1
reply
1.3k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks
WGCNA
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
txtbookir
• 0
0
votes
0
replies
709
views
DEGs for legacy and harmonized dataset
#DEGs
#legacydataset
#harmonizeddataset
TCGAbiolinks
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
Gisele
• 0
0
votes
1
reply
1.1k
views
Help With TCGAbiolinks package
TCGAbiolinks
data
normalize
l
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
DANIELA
• 0
0
votes
2
replies
1.1k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
2.9 years ago
H. Z. Amini
▴ 10
0
votes
0
replies
1.6k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks
TCGAWorkflowData
2.9 years ago
H. Z. Amini
▴ 10
0
votes
0
replies
727
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
3.0 years ago
rebeliscu
• 0
0
votes
3
replies
929
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
3.0 years ago
xiaofeiwang18266
▴ 50
1
vote
1
reply
1.4k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
xiaofeiwang18266
▴ 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
0
replies
844
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
806
views
library(TCGAbiolinks)
TCGAbiolinks
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
1664424607
• 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
0
votes
1
reply
902
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 3.4 years ago by
shepherl
3.8k • written 3.4 years ago by
sbetrosian
• 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
biologsr
• 0 • written 3.6 years ago by
aush
▴ 40
0
votes
5
replies
2.0k
views
TCGA: to extract clinical data from barcode
cancer
TCGAbiolinks
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
Marie DENIS
▴ 10
0
votes
5
replies
2.7k
views
Retrieve TCGA expression data for a single gene
TCGA
TCGAbiolinks
updated 3.6 years ago by
Tiago Chedraoui Silva
▴ 260 • written 3.7 years ago by
aush
▴ 40
4
votes
6
replies
1.7k
views
TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
3.7 years ago
mario.zanfardino
▴ 160
50 results • Page
1 of 1
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Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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