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tcgabiolinks
•
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0
votes
1
reply
210
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
136
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
152
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
150
views
GDC slides download
TCGAbiolinks
9 weeks ago
jain72744
• 0
0
votes
4
replies
270
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
143
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
11 weeks ago
Thalita
• 0
0
votes
1
reply
375
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
6 months ago
leon
• 0
0
votes
0
replies
241
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
842
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
12 months ago
qiz218591
• 0
1
vote
1
reply
752
views
Error when running getGDCprojects()
TCGAbiolinks
13 months ago
DevelopingHippo
• 0
0
votes
1
reply
606
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
531
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
923
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
15 months ago
Alexandre
• 0
0
votes
0
replies
455
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
17 months ago
lescano
▴ 10
0
votes
0
replies
628
views
Query on TCGA
TCGAbiolinks
TCGAWorkflow
19 months ago
hemangininaik09
• 0
0
votes
0
replies
716
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
21 months ago
qiz218591
• 0
0
votes
0
replies
516
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
534
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks
TCGAbiolinksGUI.data
SummarizedExperiment
23 months ago
syednajeebashraf
• 0
0
votes
4
replies
969
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 8 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 24 months ago by
Tiago C. Silva
▴ 270 • written 2.0 years ago by
Лиза
• 0
0
votes
0
replies
563
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
797
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.4 years ago
constantinosdem
• 0
0
votes
0
replies
666
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
702
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
720
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
2.9 years ago
rebeliscu
• 0
0
votes
3
replies
924
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
3.1 years ago • updated 3.0 years ago
xiaofeiwang18266
▴ 50
0
votes
0
replies
842
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
802
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
898
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 3.6 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
Recent ...
Replies
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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ATpoint
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Gordon Smyth
50k
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i.sudbery
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Michael Love
41k
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shepherl
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