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tcgabiolinks
•
reset
5
votes
4
replies
337
views
HTSeq Counts no longer available
TCGAbiolinks
updated 8 days ago by
swbarnes2
★ 1.0k • written 7 weeks ago by
vm
▴ 30
0
votes
0
replies
41
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
TCGAutils
25 days ago • updated 24 days ago
Emre
• 0
0
votes
2
replies
220
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks
TARGET-AML
updated 27 days ago by
Tiago C. Silva
▴ 210 • written 5 weeks ago by
Лиза
• 0
0
votes
1
reply
138
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 27 days ago by
Tiago C. Silva
▴ 210 • written 4 weeks ago by
mahsa
• 0
3
votes
2
replies
943
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 5 weeks ago by
cute scientist
• 0 • written 3.5 years ago by
Antonio Ahn
▴ 10
2
votes
5
replies
543
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 4 weeks ago by
biologsr
• 0 • written 20 months ago by
aush
▴ 40
0
votes
0
replies
76
views
GDCquery error when querying mutect2 data
TCGAbiolinks
6 weeks ago
komal.rathi
▴ 100
0
votes
1
reply
166
views
GDCprepare() - R Session Aborted
TCGAbiolinks
R
GDCprepare()
updated 6 weeks ago by
Tiago C. Silva
▴ 210 • written 6 weeks ago by
spyrouglykeria
• 0
5
votes
3
replies
668
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 5 weeks ago by
Nikolas
• 0 • written 7 weeks ago by
lescano
▴ 10
2
votes
7
replies
878
views
GDCquery_Maf error
TCGAbiolinks
GDCquery_Maf
updated 7 weeks ago by
Benedek
▴ 20 • written 7 weeks ago by
e.iich
• 0
0
votes
0
replies
175
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
5 months ago
constantinosdem
• 0
0
votes
0
replies
156
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq
TCGAbiolinks
TCGAAnalyze_DEA
6 months ago
Gandino
• 0
0
votes
1
reply
347
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
6 months ago
raf4
▴ 20
1
vote
2
replies
258
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks
cnv
7 months ago • updated 6 months ago
raf4
▴ 20
0
votes
1
reply
256
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks
WGCNA
updated 9 months ago by
Michael Love
37k • written 9 months ago by
txtbookir
• 0
0
votes
7
replies
2.0k
views
GDCquery(project = "TCGA-COAD") did not work; but GDCquery(project = "TCGA-READ") workl why???
gdcquery
tcgabiolinks
updated 9 months ago by
Jessica
• 0 • written 4.0 years ago by
hwteng1971
• 0
0
votes
0
replies
142
views
DEGs for legacy and harmonized dataset
#DEGs
#legacydataset
#harmonizeddataset
TCGAbiolinks
updated 9 months ago by
Kevin Blighe
3.5k • written 9 months ago by
Gisele
• 0
0
votes
1
reply
248
views
Help With TCGAbiolinks package
TCGAbiolinks
data
normalize
l
updated 9 months ago by
Kevin Blighe
3.5k • written 9 months ago by
DANIELA
• 0
0
votes
2
replies
342
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
11 months ago
H. Z. Amini
• 0
0
votes
0
replies
496
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks
TCGAWorkflowData
11 months ago
H. Z. Amini
• 0
0
votes
0
replies
196
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
12 months ago
rebeliscu
• 0
0
votes
3
replies
314
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
13 months ago
xiaofeiwang18266
▴ 40
1
vote
1
reply
442
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 13 months ago by
Michael Love
37k • written 13 months ago by
xiaofeiwang18266
▴ 40
3
votes
8
replies
1.3k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
13 months ago
xiaofeiwang18266
▴ 40
0
votes
0
replies
290
views
Job:
Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks
BiomedicalInformatics
Network
14 months ago
martin.schaefer
• 0
0
votes
1
reply
289
views
library(TCGAbiolinks)
TCGAbiolinks
updated 16 months ago by
Kevin Blighe
3.5k • written 16 months ago by
1664424607
• 0
3
votes
7
replies
3.4k
views
how to add a new column in colData in SummarizedExperiment
summarizedexperiment
tcgabiolinks
written 3.9 years ago by
hwteng1971
• 0
0
votes
1
reply
354
views
TCGAbiolinks connection error for GDCquery
MethylationArray
TCGAbiolinks
16 months ago • updated 15 months ago
Sophie Marion de Proce
• 0
0
votes
1
reply
282
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 17 months ago by
shepherl
3.1k • written 17 months ago by
sbetrosian
• 0
0
votes
5
replies
539
views
TCGA: to extract clinical data from barcode
cancer
TCGAbiolinks
updated 20 months ago by
Kevin Blighe
3.5k • written 20 months ago by
Marie DENIS
▴ 10
0
votes
5
replies
650
views
Retrieve TCGA expression data for a single gene
TCGA
TCGAbiolinks
updated 21 months ago by
Tiago Chedraoui Silva
▴ 260 • written 21 months ago by
aush
▴ 40
4
votes
6
replies
541
views
TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
21 months ago
mario.zanfardino
▴ 160
0
votes
5
replies
523
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks
R.oo
updated 4 months ago by
ersan
• 0 • written 22 months ago by
Talip Zengin
▴ 10
0
votes
2
replies
963
views
TCGAbiolinks BioMart error
TCGAbiolinks
BioMart
updated 22 months ago by
James W. MacDonald
59k • written 22 months ago by
Talip Zengin
▴ 10
1
vote
3
replies
1.9k
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation
permission denied
RTCGAToolbox
TCGAbiolinks
2.0 years ago
julia.tutzauer
• 0
0
votes
0
replies
289
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks
filtering
gdc
TCGABiolinks
rnaseq
2.3 years ago
jam526
• 0
0
votes
1
reply
1.3k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks
Methylation
GDC data
Data prepare
2.4 years ago
ph.shimaasherif
• 0
0
votes
0
replies
431
views
Error in downloading the MAF file for the TARGET data
TCGAbiolinks
TARGET
MAF
2.4 years ago
ph.shimaasherif
• 0
2
votes
4
replies
461
views
Error : Results must have the same dimensions
TCGAbiolinks
GDC dataset
2.4 years ago
ph.shimaasherif
• 0
0
votes
0
replies
309
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks
GDC
TCGA
2.4 years ago
modarzi
▴ 10
0
votes
4
replies
467
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks
TCGA
GDC
2.5 years ago
modarzi
▴ 10
1
vote
3
replies
610
views
Missing Clinical LIHC Data
Missing Data
TCGAbiolinks
Kaplan-Meier
LIHC
Xenabrowser
2.5 years ago
jam526
• 0
0
votes
0
replies
540
views
GDCprepare error in TCGAbiolinks
tcgabiolinks
gdcprepare
differential expression
2.6 years ago
fawazfebin
▴ 30
0
votes
1
reply
374
views
error reading from connection
TCGAbiolinks
updated 13 months ago by
Kevin Blighe
3.5k • written 2.6 years ago by
471555750
• 0
5
votes
11
replies
1.8k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 2.9 years ago by
Marcel Ramos
570 • written 2.9 years ago by
Dario Strbenac
★ 1.5k
4
votes
5
replies
1.3k
views
GDCprepare - error
TCGABiolinks
GDCprepare
2.9 years ago
vm
▴ 30
2
votes
2
replies
910
views
TCGAbiolinks GDCprepare error
TCGAbiolinks
GDCprepare
error
updated 2.9 years ago by
Tiago C. Silva
▴ 210 • written 2.9 years ago by
Talip Zengin
▴ 10
1
vote
2
replies
465
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga
bisulfite
tcgabiolinks
updated 2.9 years ago by
Tiago Chedraoui Silva
▴ 260 • written 2.9 years ago by
DS
• 0
0
votes
1
reply
751
views
Downloading HTSeq raw reads with TCGABiolinks
TCGAbiolinks
RNASEQ
2.9 years ago
sherajilir
• 0
2
votes
4
replies
722
views
Missing clinical data at TCGAbiolinks data
TCGAbiolinks
days_to_death
clinical data
missing column
updated 3.1 years ago by
Tiago Chedraoui Silva
▴ 260 • written 3.1 years ago by
Talip Zengin
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: CPM after RUVseq
by
James W. MacDonald
59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq
by
James W. MacDonald
59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq
by
Jess
• 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error
by
Laurent Gatto
1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue
by
shepherl
3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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