Showing : tcga • reset
6
votes
7
replies
2.4k
views
Download TCGA dataset like a S4 object
dataset tcga
updated 7.2 years ago by ▴ 160 • written 7.2 years ago by ▴ 20
0
votes
0
replies
1.3k
views
Noise Analyses of CNV Data from TCGA
tcgabiolinks tcga cnv noise pruning
7.3 years ago jrlarsen ▴ 10
8
votes
5
replies
2.6k
views
Querying specific TCGA datasets through the MultiAssayExperiment R package
MultiAssayExperiment curatedCRCdata multiomics TCGA
updated 7.3 years ago by 700 • written 7.3 years ago by ▴ 840
2
votes
1
reply
2.6k
views
Error in TCGAquery of TCGAbiolinks Package
software error bioconductor tcgabiolinks tcga r
updated 7.4 years ago by ▴ 90 • written 7.4 years ago by ▴ 60
1
vote
0
replies
1.8k
views
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
deseq2 tcga
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
3
votes
3
replies
2.1k
views
Retrieve accurate tumor stage data with TCGAbiolinks
tcgabiolinks tcga
7.4 years ago Benjamin Ostendorf ▴ 90
19
votes
8
replies
4.3k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 7.5 years ago by 21k • written 7.5 years ago by ▴ 120
6
votes
14
replies
4.0k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 7.5 years ago by ▴ 840 • written 7.5 years ago by ▴ 30
0
votes
2
replies
3.9k
views
Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 7.5 years ago by • 0 • written 10.5 years ago by • 0
3
votes
2
replies
1.4k
views
Can i add an experiment to an existing MultiAssayExperiment?
mutiassayexperiment tcga tcia
7.6 years ago mario.zanfardino ▴ 160
0
votes
2
replies
1.5k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 7.6 years ago by • 0 • written 7.6 years ago by • 0
0
votes
0
replies
1.5k
views
How to get disease free survival information from TCGA using TCGAbiolinks?
tcgabiolinks tcga
7.6 years ago Frocha ▴ 20
2
votes
1
reply
5.4k
views
Using DESeq2 to analyse TCGA data
deseq2 tcga tcgabiolinks gene expression differential expression
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
vote
2
replies
2.1k
views
DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2 design TCGA unpaired RNAseq
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
0
votes
4
replies
2.0k
views
how to reformat complex list object (derived with TCGAbiolinks)?
TCGA tcgabiolinks list reformat
7.8 years ago Guido Hooiveld ★ 4.1k
0
votes
0
replies
1.7k
views
Specific considerations in RNA-Seq DE analysis with edgeR pipeline for a TCGA dataset starting with HTSeq counts
edgeR rnaseq DEanalysis TCGA independent filtering
7.9 years ago svlachavas ▴ 840
1
vote
7
replies
2.9k
views
Cannot retrieve projects from TCGA using getGDCprojects function
tcgabiolinks TCGA software error
7.9 years ago jacorvar ▴ 40
0
votes
2
replies
24k
views
Determining gene expression levels with DESeq2 in a design with no condition
deseq2 tcga
7.9 years ago robles.daniela • 0
2
votes
2
replies
3.0k
views
TCGAbiolinks Download ERROR
TCGA tcgabiolinks download error
updated 7.9 years ago by ▴ 40 • written 7.9 years ago by ▴ 10
0
votes
4
replies
2.5k
views
DEseq2: any problem with unbalanced number of sample in normal/tumor study?
deseq2 rnaseq tcga
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
0
votes
3
replies
1.8k
views
TCGAvisualize_EAbarplot Function Issue
tcga
updated 8.0 years ago by ▴ 40 • written 9.6 years ago by • 0
0
votes
0
replies
782
views
differentially expressed miRNA from TCGA miRna seq data
tcga
8.0 years ago lily ▴ 20
1
vote
2
replies
3.8k
views
DESeq2/edgeR DEG analysis data input from TCGA and correation analysis
edgeR TCGA
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
0
votes
1
reply
1.6k
views
Error downloading the package
tcgabiolinks TCGA DOWNLOAD
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 30
0
votes
0
replies
1.0k
views
Error in mRNAselected_values_ordered[1:(lastelementTOP - 1)]
tcgabiolinks TCGA survival analysis
8.1 years ago lqfuture • 0
2
votes
0
replies
4.7k
views
Tutorial: BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor
public data TCGA GTEx Tutorial
8.2 years ago shepherl 4.2k
1
vote
3
replies
3.4k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 8.2 years ago by 68k • written 8.2 years ago by ▴ 120
0
votes
3
replies
2.1k
views
Analysing TCGA Level 3 Copy Number Data Location of markers in the genome
TCGA Cancer dnacopy segmentation
updated 8.3 years ago by ▴ 130 • written 8.3 years ago by • 0
0
votes
2
replies
4.0k
views
Error using TCGAbiolinks "Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column"
TCGA tcgabiolinks Error
8.3 years ago f.geist ▴ 20
2
votes
2
replies
1.8k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 8.3 years ago by ★ 1.1k • written 8.3 years ago by ▴ 20
1
vote
0
replies
2.2k
views
Problem about module preservation statistics in WGCNA software
rnaseq tcga wgcna
8.5 years ago • updated 8.4 years ago panagiotis.mokos ▴ 40
0
votes
2
replies
4.5k
views
Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 8.5 years ago by ▴ 260 • written 8.7 years ago by • 0
0
votes
0
replies
3.0k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
8.6 years ago panagiotis.mokos ▴ 40
3
votes
12
replies
4.7k
views
Problem about use of TCGA rna-seq rsem gene results for regularized cox regression modeling
tcga rnaseq glmnet voom deseq2
8.6 years ago panagiotis.mokos ▴ 40
25
votes
37
replies
15k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq RSEM TCGA edgeR normalization
updated 8.7 years ago by 53k • written 8.7 years ago by ▴ 840
0
votes
1
reply
1.1k
views
TCGA Lung Cancer Pulmonary Function Test Data
tcga lusc luad pft pulmonary function test
8.8 years ago zyr123 • 0
1
vote
4
replies
2.7k
views
Error on creation of DESEq2 object
deseq2 tcga
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 40
0
votes
0
replies
1.4k
views
how to annotate TCGA snp6 data with genomic coordinates
microarray tcga annotation snp6.0
9.0 years ago seeker • 0
0
votes
4
replies
1.9k
views
TCGABiolinks not available for R3.3.0
TCGA tcgabiolinks R
updated 9.3 years ago by 25k • written 9.3 years ago by • 0
2
votes
6
replies
2.6k
views
Using TCGAbiolinks for exon and oligonucleotide level microarray
tcga tcgabiolinks microarray exons oligonucleotide
updated 9.4 years ago by ▴ 270 • written 9.4 years ago by • 0
0
votes
1
reply
1.7k
views
LuminalA Breast cancer subtype samples from GEO GSE62944
tcga cancer BreastCancer gse62944 luminalA
updated 9.5 years ago by ▴ 150 • written 9.5 years ago by • 0
0
votes
2
replies
1.6k
views
Differential gene expression analysis for GSE62944
R limma cancer tcga bioconductor
updated 9.5 years ago by ★ 6.8k • written 9.5 years ago by • 0
0
votes
0
replies
920
views
TCGAvisualize_EAbarplot Function Issues, won't produce expected charts
TCGA
9.6 years ago pgreylin • 0
0
votes
2
replies
2.1k
views
mutational signatures problems
bsgenome readvcf tcga annotation somaticsignatures
updated 12 months ago by • 0 • written 9.6 years ago by • 0
1
vote
3
replies
5.0k
views
R Text progress bar error
TCGA
9.8 years ago devyani66 • 0
0
votes
3
replies
1.9k
views
Mapping of two different regions to one gene symbol
TCGA CNV
updated 10.4 years ago by ★ 7.2k • written 10.4 years ago by ▴ 60
4
votes
3
replies
3.3k
views
DESeq2 - design for TCGA level 3 data
deseq2 tcga experimental design multiple factor design
updated 10.4 years ago by 43k • written 10.4 years ago by ▴ 40
0
votes
0
replies
931
views
RNAseq binary transformation
tcga binary rnaseq
10.4 years ago ezz • 0
1
vote
4
replies
3.9k
views
Different clustering results of DESeq2 counts and rlog
tcga nomalization rnaseq deseq2
10.4 years ago ezz • 0
0
votes
2
replies
3.7k
views
Pipeline for analyzing CNV (SNP array) level 3 from TCGA
SNP CNV TCGA
10.5 years ago NS ▴ 60
105 results • Page 2 of 3
Recent ...
Replies
Comment: PCA subset of genes vs DE by Ben • 0
PCA evaluates separation according to your input. The subset of genes you used may be entirely identical in terms of expression, indicatin…
Comment: Problem with MakeTxDbFromGFF by Ben • 0
Wow can't believe he can really answer this [speed stars][1] [1]: https://speed-stars.co
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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