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TCGAbiolinks
•
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0
votes
0
replies
168
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
10 weeks ago • updated 8 weeks ago
Giovanni Calice
▴ 160
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 8 weeks ago by
snijesh
▴ 20 • written 6.6 years ago by
Ramiro Magno
▴ 100
0
votes
1
reply
251
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 9 weeks ago by
BioinfoMug
• 0
1
vote
0
replies
187
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
11 weeks ago
BioinfoMug
• 0
0
votes
4
replies
1.0k
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 12 weeks ago by
Marcel Ramos
700 • written 2.1 years ago by
Emre
• 0
0
votes
0
replies
180
views
GDC slides download
TCGAbiolinks
3 months ago
jain72744
• 0
0
votes
4
replies
320
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 3 months ago by
Lluís Revilla Sancho
▴ 730 • written 3 months ago by
tirordep
• 0
0
votes
0
replies
172
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
3 months ago
Thalita
• 0
0
votes
1
reply
431
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
6 months ago
leon
• 0
0
votes
1
reply
633
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 9 months ago by
wrab425
• 0 • written 14 months ago by
snijesh
▴ 20
0
votes
0
replies
259
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical
TCGAbiolinks
10 months ago
BioInfoBeginnerrr
• 0
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
12 months ago • updated 11 months ago
Habil Zare
▴ 200
0
votes
2
replies
888
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
13 months ago • updated 12 months ago
qiz218591
• 0
1
vote
1
reply
796
views
Error when running getGDCprojects()
TCGAbiolinks
14 months ago
DevelopingHippo
• 0
0
votes
0
replies
583
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
14 months ago
Manav
• 0
1
vote
2
replies
1.6k
views
Error when running GDC_prepare
TCGAbiolinks
14 months ago
DevelopingHippo
• 0
1
vote
3
replies
960
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
16 months ago
Alexandre
• 0
0
votes
0
replies
472
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()
2.1 years ago • updated 19 months ago
spyrouglykeria
• 0
0
votes
1
reply
1.9k
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 20 months ago by
Aurora
• 0 • written 2.1 years ago by
mahsa
• 0
0
votes
0
replies
656
views
Query on TCGA
TCGAbiolinks
TCGAWorkflow
20 months ago
hemangininaik09
• 0
0
votes
2
replies
1.4k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
updated 21 months ago by
Tiago C. Silva
▴ 270 • written 23 months ago by
JAcky
• 0
2
votes
8
replies
4.9k
views
GDCquery_Maf error
TCGAbiolinks
GDCquery_Maf
updated 22 months ago by
1526466763
• 0 • written 2.1 years ago by
e.iich
• 0
0
votes
0
replies
754
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
22 months ago
qiz218591
• 0
0
votes
0
replies
540
views
TCGAbiolinks file.type argument
TCGAbiolinks
22 months ago
Elizabeth
• 0
0
votes
0
replies
551
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks
TCGAbiolinksGUI.data
SummarizedExperiment
23 months ago
syednajeebashraf
• 0
5
votes
4
replies
2.9k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 2.0 years ago by
swbarnes2
★ 1.4k • written 2.1 years ago by
vm
▴ 30
0
votes
2
replies
2.1k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks
TARGET-AML
updated 2.1 years ago by
Tiago C. Silva
▴ 270 • written 2.1 years ago by
Лиза
• 0
2
votes
5
replies
1.6k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 2.1 years ago by
biologsr
• 0 • written 3.7 years ago by
aush
▴ 40
3
votes
2
replies
2.2k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 2.1 years ago by
cute scientist
• 0 • written 5.5 years ago by
Antonio Ahn
▴ 10
6
votes
3
replies
3.2k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.1 years ago by
Nikolas
• 0 • written 2.1 years ago by
lescano
▴ 10
0
votes
0
replies
584
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.1 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 3.8 years ago by
Talip Zengin
▴ 10
0
votes
0
replies
829
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.4 years ago
constantinosdem
• 0
0
votes
0
replies
677
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq
TCGAbiolinks
TCGAAnalyze_DEA
2.5 years ago
Gandino
• 0
0
votes
1
reply
2.2k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
2.5 years ago
raf4
▴ 20
1
vote
2
replies
1.1k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks
cnv
2.6 years ago • updated 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
42k • written 2.7 years ago by
txtbookir
• 0
0
votes
0
replies
746
views
DEGs for legacy and harmonized dataset
#DEGs
#legacydataset
#harmonizeddataset
TCGAbiolinks
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
Gisele
• 0
0
votes
1
reply
1.2k
views
Help With TCGAbiolinks package
TCGAbiolinks
data
normalize
l
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
DANIELA
• 0
0
votes
2
replies
1.2k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
3.0 years ago
H. Z. Amini
▴ 10
0
votes
0
replies
1.6k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks
TCGAWorkflowData
3.0 years ago
H. Z. Amini
▴ 10
0
votes
3
replies
4.3k
views
Problem in downloading data via TCGAbiolinks
tcgabiolinks
tcgadownload
updated 3.0 years ago by
H. Z. Amini
▴ 10 • written 7.8 years ago by
sabarinath.chandrasekharan
▴ 10
0
votes
0
replies
741
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
3.0 years ago
rebeliscu
• 0
0
votes
3
replies
950
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
3.1 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 3.1 years ago by
Michael Love
42k • written 3.1 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
xiaofeiwang18266
▴ 50
0
votes
1
reply
774
views
error reading from connection
TCGAbiolinks
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 4.6 years ago by
471555750
• 0
0
votes
0
replies
857
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
Sophie Marion de Proce
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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