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TCGAbiolinks
•
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0
votes
1
reply
191
views
combining raw counts and estimated counts
RNASeqData
GEO
TCGAbiolinks
updated 4 weeks ago by
O'Brien
• 0 • written 5 weeks ago by
Noor
• 0
0
votes
7
replies
1.0k
views
How should I know which platforms are available for TCGA methylation?
TCGAbiolinks
updated 12 weeks ago by
James W. MacDonald
67k • written 3 months ago by
xiaofeiwang198266
• 0
3
votes
3
replies
3.7k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 10 months ago by
snijesh
▴ 200 • written 7.3 years ago by
Ramiro Magno
▴ 100
0
votes
0
replies
430
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
10 months ago
Giovanni Calice
▴ 160
0
votes
0
replies
475
views
GDC slides download
TCGAbiolinks
11 months ago
jain72744
• 0
0
votes
4
replies
693
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 11 months ago by
Lluís Revilla Sancho
▴ 760 • written 11 months ago by
tirordep
• 0
0
votes
0
replies
476
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
12 months ago
Thalita
• 0
0
votes
1
reply
900
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
15 months ago
leon
• 0
0
votes
0
replies
422
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical
TCGAbiolinks
18 months ago
BioInfoBeginnerrr
• 0
4
votes
8
replies
1.6k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
20 months ago
Habil Zare
▴ 200
0
votes
2
replies
1.3k
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
22 months ago • updated 21 months ago
qiz218591
• 0
1
vote
1
reply
1.1k
views
Error when running getGDCprojects()
TCGAbiolinks
22 months ago
DevelopingHippo
• 0
2
votes
1
reply
953
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 17 months ago by
wrab425
• 0 • written 23 months ago by
snijesh
▴ 200
0
votes
0
replies
942
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
23 months ago
Manav
• 0
1
vote
2
replies
2.1k
views
Error when running GDC_prepare
TCGAbiolinks
23 months ago
DevelopingHippo
• 0
1
vote
3
replies
1.3k
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
2.1 years ago
Alexandre
• 0
0
votes
0
replies
667
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
2.2 years ago
lescano
▴ 10
0
votes
0
replies
894
views
Query on TCGA
TCGAbiolinks
TCGAWorkflow
2.4 years ago
hemangininaik09
• 0
0
votes
2
replies
1.9k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
updated 2.5 years ago by
Tiago C. Silva
▴ 270 • written 2.6 years ago by
JAcky
• 0
0
votes
0
replies
1.0k
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
2.5 years ago
qiz218591
• 0
0
votes
0
replies
712
views
TCGAbiolinks file.type argument
TCGAbiolinks
2.5 years ago
Elizabeth
• 0
0
votes
0
replies
704
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks
TCGAbiolinksGUI.data
SummarizedExperiment
2.7 years ago
syednajeebashraf
• 0
5
votes
4
replies
3.6k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 2.7 years ago by
swbarnes2
★ 1.4k • written 2.8 years ago by
vm
▴ 30
0
votes
4
replies
1.4k
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 11 months ago by
Marcel Ramos
700 • written 2.8 years ago by
Emre
• 0
0
votes
2
replies
2.4k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks
TARGET-AML
updated 2.8 years ago by
Tiago C. Silva
▴ 270 • written 2.8 years ago by
Лиза
• 0
0
votes
1
reply
2.2k
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 2.4 years ago by
Aurora
• 0 • written 2.8 years ago by
mahsa
• 0
3
votes
2
replies
2.5k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 2.8 years ago by
cute scientist
• 0 • written 6.2 years ago by
Antonio Ahn
▴ 10
4
votes
5
replies
1.9k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 2.8 years ago by
biologsr
• 0 • written 4.4 years ago by
aush
▴ 40
0
votes
0
replies
812
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.8 years ago
komal.rathi
▴ 120
0
votes
2
replies
2.5k
views
GDCprepare() - R Session Aborted
TCGAbiolinks
R
GDCprepare()
2.8 years ago • updated 2.3 years ago
spyrouglykeria
• 0
6
votes
3
replies
3.6k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.8 years ago by
Nikolas
• 0 • written 2.8 years ago by
lescano
▴ 10
2
votes
8
replies
5.9k
views
GDCquery_Maf error
TCGAbiolinks
GDCquery_Maf
updated 2.5 years ago by
1526466763
• 0 • written 2.8 years ago by
e.iich
• 0
0
votes
0
replies
1.0k
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
3.1 years ago
constantinosdem
• 0
0
votes
0
replies
934
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq
TCGAbiolinks
TCGAAnalyze_DEA
3.2 years ago
Gandino
• 0
0
votes
1
reply
2.6k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
3.2 years ago
raf4
▴ 30
1
vote
2
replies
1.5k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks
cnv
3.3 years ago • updated 3.2 years ago
raf4
▴ 30
0
votes
1
reply
1.8k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks
WGCNA
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
txtbookir
• 0
0
votes
0
replies
971
views
DEGs for legacy and harmonized dataset
#DEGs
#legacydataset
#harmonizeddataset
TCGAbiolinks
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
Gisele
• 0
0
votes
1
reply
1.4k
views
Help With TCGAbiolinks package
TCGAbiolinks
data
normalize
l
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
DANIELA
• 0
0
votes
2
replies
1.5k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
3.7 years ago
H. Z. Amini
▴ 10
0
votes
0
replies
2.0k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks
TCGAWorkflowData
3.7 years ago
H. Z. Amini
▴ 10
0
votes
0
replies
958
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
3.7 years ago
rebeliscu
• 0
0
votes
3
replies
1.2k
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
3.8 years ago
xiaofeiwang18266
▴ 50
1
vote
1
reply
1.7k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 3.8 years ago by
Michael Love
43k • written 3.8 years ago by
xiaofeiwang18266
▴ 50
3
votes
8
replies
4.0k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
3.8 years ago
xiaofeiwang18266
▴ 50
0
votes
0
replies
1.0k
views
Job:
Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks
BiomedicalInformatics
Network
3.8 years ago
martin.schaefer
• 0
0
votes
1
reply
1.0k
views
library(TCGAbiolinks)
TCGAbiolinks
updated 4.0 years ago by
Kevin Blighe
★ 4.0k • written 4.0 years ago by
1664424607
• 0
0
votes
1
reply
2.2k
views
TCGAbiolinks connection error for GDCquery
MethylationArray
TCGAbiolinks
4.0 years ago
Sophie Marion de Proce
• 0
0
votes
1
reply
1.2k
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 4.1 years ago by
shepherl
4.1k • written 4.1 years ago by
sbetrosian
• 0
0
votes
5
replies
3.0k
views
TCGA: to extract clinical data from barcode
cancer
TCGAbiolinks
updated 4.4 years ago by
Kevin Blighe
★ 4.0k • written 4.4 years ago by
Marie DENIS
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Prakash Sah
• 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
ATpoint
★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
Votes
Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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