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tcgabiolinks
•
reset
1
vote
2
replies
320
views
How to install packages such as TCGAbiolinks, SumarizedExperiment?
TCGAbiolinks
SummarizedExperiment
written 5 weeks ago by
NewRUser
• 0
1
vote
1
reply
1.4k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression
TCGAbiolinks
RNASeq
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
Shaimaa Gamal
• 0
1
vote
2
replies
1.8k
views
Error in retrieving clinical data
TCGAbiolinks
11 months ago • updated 10 months ago
silickas
• 0
0
votes
1
reply
739
views
combining raw counts and estimated counts
RNASeqData
GEO
TCGAbiolinks
updated 13 months ago by
O'Brien
• 0 • written 13 months ago by
Noor
• 0
0
votes
7
replies
1.8k
views
How should I know which platforms are available for TCGA methylation?
TCGAbiolinks
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
xiaofeiwang198266
• 0
3
votes
3
replies
4.4k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 22 months ago by
snijesh
▴ 200 • written 8.3 years ago by
Ramiro Magno
▴ 100
0
votes
0
replies
649
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
23 months ago • updated 22 months ago
Giovanni Calice
▴ 160
0
votes
0
replies
1.5k
views
GDC slides download
TCGAbiolinks
23 months ago
jain72744
• 0
0
votes
4
replies
1.6k
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 24 months ago by
Lluís Revilla Sancho
▴ 760 • written 24 months ago by
tirordep
• 0
0
votes
0
replies
726
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
2.0 years ago
Thalita
• 0
0
votes
1
reply
1.8k
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
2.3 years ago
leon
• 0
0
votes
0
replies
745
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical
TCGAbiolinks
2.6 years ago
BioInfoBeginnerrr
• 0
4
votes
8
replies
2.3k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
2.7 years ago
Habil Zare
▴ 200
0
votes
2
replies
1.9k
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
2.8 years ago
qiz218591
• 0
1
vote
1
reply
1.4k
views
Error when running getGDCprojects()
TCGAbiolinks
2.9 years ago
DevelopingHippo
• 0
2
votes
1
reply
1.6k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 2.5 years ago by
wrab425
• 0 • written 2.9 years ago by
snijesh
▴ 200
0
votes
0
replies
1.4k
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
2.9 years ago
Manav
• 0
1
vote
2
replies
2.8k
views
Error when running GDC_prepare
TCGAbiolinks
2.9 years ago
DevelopingHippo
• 0
1
vote
3
replies
1.8k
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
3.1 years ago
Alexandre
• 0
0
votes
0
replies
891
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
3.3 years ago
lescano
▴ 10
0
votes
0
replies
1.2k
views
Query on TCGA
TCGAbiolinks
TCGAWorkflow
3.4 years ago
hemangininaik09
• 0
0
votes
2
replies
3.0k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
updated 3.5 years ago by
Tiago C. Silva
▴ 270 • written 3.6 years ago by
JAcky
• 0
0
votes
0
replies
1.4k
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
3.5 years ago
qiz218591
• 0
0
votes
0
replies
1.1k
views
TCGAbiolinks file.type argument
TCGAbiolinks
3.5 years ago
Elizabeth
• 0
0
votes
0
replies
936
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks
TCGAbiolinksGUI.data
SummarizedExperiment
3.7 years ago
syednajeebashraf
• 0
5
votes
4
replies
5.4k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 3.7 years ago by
swbarnes2
★ 1.4k • written 3.8 years ago by
vm
▴ 30
0
votes
4
replies
2.0k
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 23 months ago by
Marcel Ramos
700 • written 3.8 years ago by
Emre
• 0
0
votes
2
replies
2.9k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks
TARGET-AML
updated 3.8 years ago by
Tiago C. Silva
▴ 270 • written 3.8 years ago by
Лиза
• 0
0
votes
1
reply
2.6k
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 3.4 years ago by
Aurora
• 0 • written 3.8 years ago by
mahsa
• 0
3
votes
2
replies
3.9k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 3.8 years ago by
cute scientist
• 0 • written 7.2 years ago by
Antonio Ahn
▴ 10
4
votes
5
replies
2.4k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 3.8 years ago by
biologsr
• 0 • written 5.4 years ago by
aush
▴ 40
0
votes
0
replies
1.3k
views
GDCquery error when querying mutect2 data
TCGAbiolinks
3.8 years ago
komal.rathi
▴ 120
0
votes
2
replies
2.9k
views
GDCprepare() - R Session Aborted
TCGAbiolinks
R
GDCprepare()
3.8 years ago • updated 3.3 years ago
spyrouglykeria
• 0
6
votes
3
replies
4.2k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 3.8 years ago by
Nikolas
• 0 • written 3.8 years ago by
lescano
▴ 10
2
votes
8
replies
6.8k
views
GDCquery_Maf error
TCGAbiolinks
GDCquery_Maf
updated 3.5 years ago by
1526466763
• 0 • written 3.9 years ago by
e.iich
• 0
0
votes
1
reply
1.7k
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
updated 11 months ago by
Jane
• 0 • written 4.1 years ago by
constantinosdem
• 0
0
votes
0
replies
1.3k
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq
TCGAbiolinks
TCGAAnalyze_DEA
4.2 years ago
Gandino
• 0
0
votes
1
reply
3.2k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
4.2 years ago
raf4
▴ 30
1
vote
2
replies
2.2k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks
cnv
4.3 years ago • updated 4.2 years ago
raf4
▴ 30
0
votes
1
reply
2.2k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks
WGCNA
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
txtbookir
• 0
0
votes
0
replies
1.2k
views
DEGs for legacy and harmonized dataset
#DEGs
#legacydataset
#harmonizeddataset
TCGAbiolinks
updated 4.5 years ago by
Kevin Blighe
★ 4.0k • written 4.5 years ago by
Gisele
• 0
0
votes
1
reply
1.9k
views
Help With TCGAbiolinks package
TCGAbiolinks
data
normalize
l
updated 4.5 years ago by
Kevin Blighe
★ 4.0k • written 4.5 years ago by
DANIELA
• 0
0
votes
2
replies
2.0k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
4.7 years ago
H. Z. Amini
▴ 10
0
votes
0
replies
3.0k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks
TCGAWorkflowData
4.7 years ago
H. Z. Amini
▴ 10
0
votes
0
replies
1.2k
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
4.7 years ago
rebeliscu
• 0
0
votes
3
replies
1.6k
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
4.8 years ago
xiaofeiwang18266
▴ 60
1
vote
1
reply
2.0k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
xiaofeiwang18266
▴ 60
3
votes
8
replies
4.8k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
4.8 years ago
xiaofeiwang18266
▴ 60
0
votes
0
replies
1.3k
views
Job:
Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks
BiomedicalInformatics
Network
4.9 years ago
martin.schaefer
• 0
0
votes
1
reply
1.3k
views
library(TCGAbiolinks)
TCGAbiolinks
updated 5.0 years ago by
Kevin Blighe
★ 4.0k • written 5.0 years ago by
1664424607
• 0
166 results • Page
1 of 4
Recent ...
Replies
Comment: using limma trend workflow in CAMERA
by
Gordon Smyth
53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results
by
Tikaaa2sahaaaq2c
• 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA
by
A.Barden
▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Tikaaa2sahaaaq2c
• 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase
by
DamionLedner99
• 0
thanks for sharing!!! https://cran.r-project.org/
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
Awards
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to
Michael Love
43k
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to
fl
▴ 20
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to
James W. MacDonald
68k
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to
rcavalca
▴ 140
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to
James Aiden
• 0
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