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TCGAbiolinks
•
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0
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0
replies
132
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
6 weeks ago • updated 4 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 4 weeks ago by
snijesh
▴ 20 • written 6.5 years ago by
Ramiro Magno
▴ 100
0
votes
1
reply
206
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 5 weeks ago by
BioinfoMug
• 0
1
vote
0
replies
143
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
7 weeks ago
BioinfoMug
• 0
0
votes
4
replies
960
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 8 weeks ago by
Marcel Ramos
690 • written 24 months ago by
Emre
• 0
0
votes
0
replies
138
views
GDC slides download
TCGAbiolinks
8 weeks ago
jain72744
• 0
0
votes
4
replies
255
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 9 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 9 weeks ago by
tirordep
• 0
0
votes
0
replies
138
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
11 weeks ago
Thalita
• 0
0
votes
1
reply
370
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
5 months ago
leon
• 0
0
votes
1
reply
600
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
238
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
834
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
12 months ago • updated 11 months ago
qiz218591
• 0
1
vote
1
reply
748
views
Error when running getGDCprojects()
TCGAbiolinks
13 months ago
DevelopingHippo
• 0
0
votes
0
replies
522
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
13 months ago
DevelopingHippo
• 0
1
vote
3
replies
915
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
15 months ago
Alexandre
• 0
0
votes
0
replies
451
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
17 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
1.8k
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 19 months ago by
Aurora
• 0 • written 24 months ago by
mahsa
• 0
0
votes
0
replies
618
views
Query on TCGA
TCGAbiolinks
TCGAWorkflow
19 months ago
hemangininaik09
• 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
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
707
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
21 months ago
qiz218591
• 0
0
votes
0
replies
508
views
TCGAbiolinks file.type argument
TCGAbiolinks
21 months ago
Elizabeth
• 0
0
votes
0
replies
530
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks
TCGAbiolinksGUI.data
SummarizedExperiment
22 months ago
syednajeebashraf
• 0
5
votes
4
replies
2.8k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 23 months ago by
swbarnes2
★ 1.3k • written 2.0 years ago by
vm
▴ 30
0
votes
2
replies
2.1k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks
TARGET-AML
updated 24 months ago by
Tiago C. Silva
▴ 270 • written 2.0 years ago by
Лиза
• 0
2
votes
5
replies
1.5k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 24 months ago by
biologsr
• 0 • written 3.6 years ago by
aush
▴ 40
3
votes
2
replies
2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 2.0 years ago by
cute scientist
• 0 • written 5.4 years ago by
Antonio Ahn
▴ 10
6
votes
3
replies
3.1k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.0 years ago by
Nikolas
• 0 • written 2.0 years ago by
lescano
▴ 10
0
votes
0
replies
554
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.0 years ago
komal.rathi
▴ 120
0
votes
5
replies
1.5k
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks
R.oo
updated 2.3 years ago by
ersan
• 0 • written 3.7 years ago by
Talip Zengin
▴ 10
0
votes
0
replies
792
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.3 years ago
constantinosdem
• 0
0
votes
0
replies
658
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
2.4 years ago
raf4
▴ 20
1
vote
2
replies
1.0k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks
cnv
2.5 years ago • updated 2.4 years ago
raf4
▴ 20
0
votes
1
reply
1.3k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks
WGCNA
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
txtbookir
• 0
0
votes
0
replies
695
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
1.5k
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
H. Z. Amini
▴ 10 • written 7.8 years ago by
sabarinath.chandrasekharan
▴ 10
0
votes
0
replies
716
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
2.9 years ago
rebeliscu
• 0
0
votes
3
replies
922
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
Michael Love
41k • written 3.0 years ago by
xiaofeiwang18266
▴ 50
3
votes
8
replies
3.4k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
3.0 years ago
xiaofeiwang18266
▴ 50
0
votes
1
reply
759
views
error reading from connection
TCGAbiolinks
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 4.5 years ago by
471555750
• 0
0
votes
0
replies
840
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
1.6k
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
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Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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