Showing : tcga • reset
6
votes
7
replies
2.8k
views
Download TCGA dataset like a S4 object
dataset tcga
updated 7.6 years ago by ▴ 160 • written 7.6 years ago by ▴ 20
0
votes
0
replies
1.7k
views
Noise Analyses of CNV Data from TCGA
tcgabiolinks tcga cnv noise pruning
7.7 years ago jrlarsen ▴ 10
8
votes
5
replies
2.8k
views
Querying specific TCGA datasets through the MultiAssayExperiment R package
MultiAssayExperiment curatedCRCdata multiomics TCGA
updated 7.7 years ago by 700 • written 7.7 years ago by ▴ 840
2
votes
1
reply
2.8k
views
Error in TCGAquery of TCGAbiolinks Package
software error bioconductor tcgabiolinks tcga r
updated 7.8 years ago by ▴ 90 • written 7.8 years ago by ▴ 60
1
vote
0
replies
2.0k
views
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
deseq2 tcga
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 10
3
votes
3
replies
2.4k
views
Retrieve accurate tumor stage data with TCGAbiolinks
tcgabiolinks tcga
7.8 years ago Benjamin Ostendorf ▴ 90
19
votes
8
replies
5.0k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 7.9 years ago by 21k • written 7.9 years ago by ▴ 120
6
votes
14
replies
4.3k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 7.9 years ago by ▴ 840 • written 7.9 years ago by ▴ 30
0
votes
2
replies
4.0k
views
Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 7.9 years ago by • 0 • written 10.9 years ago by • 0
3
votes
2
replies
1.6k
views
Can i add an experiment to an existing MultiAssayExperiment?
mutiassayexperiment tcga tcia
8.0 years ago mario.zanfardino ▴ 160
0
votes
2
replies
1.6k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 8.0 years ago by • 0 • written 8.0 years ago by • 0
0
votes
0
replies
1.6k
views
How to get disease free survival information from TCGA using TCGAbiolinks?
tcgabiolinks tcga
8.0 years ago Frocha ▴ 20
2
votes
1
reply
5.7k
views
Using DESeq2 to analyse TCGA data
deseq2 tcga tcgabiolinks gene expression differential expression
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
vote
2
replies
2.3k
views
DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2 design TCGA unpaired RNAseq
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
0
votes
4
replies
2.2k
views
how to reformat complex list object (derived with TCGAbiolinks)?
TCGA tcgabiolinks list reformat
8.1 years ago Guido Hooiveld ★ 4.1k
0
votes
0
replies
1.8k
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
8.3 years ago svlachavas ▴ 840
1
vote
7
replies
3.3k
views
Cannot retrieve projects from TCGA using getGDCprojects function
tcgabiolinks TCGA software error
8.3 years ago jacorvar ▴ 40
0
votes
2
replies
24k
views
Determining gene expression levels with DESeq2 in a design with no condition
deseq2 tcga
8.3 years ago robles.daniela • 0
2
votes
2
replies
3.2k
views
TCGAbiolinks Download ERROR
TCGA tcgabiolinks download error
updated 8.3 years ago by ▴ 40 • written 8.3 years ago by ▴ 10
0
votes
4
replies
2.7k
views
DEseq2: any problem with unbalanced number of sample in normal/tumor study?
deseq2 rnaseq tcga
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 60
0
votes
3
replies
1.9k
views
TCGAvisualize_EAbarplot Function Issue
tcga
updated 8.4 years ago by ▴ 40 • written 10.0 years ago by • 0
0
votes
0
replies
835
views
differentially expressed miRNA from TCGA miRna seq data
tcga
8.4 years ago lily ▴ 20
1
vote
2
replies
4.2k
views
DESeq2/edgeR DEG analysis data input from TCGA and correation analysis
edgeR TCGA
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Error downloading the package
tcgabiolinks TCGA DOWNLOAD
updated 8.4 years ago by 68k • written 8.4 years ago by ▴ 30
0
votes
0
replies
1.1k
views
Error in mRNAselected_values_ordered[1:(lastelementTOP - 1)]
tcgabiolinks TCGA survival analysis
8.5 years ago lqfuture • 0
2
votes
0
replies
5.0k
views
Tutorial: BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor
public data TCGA GTEx Tutorial
8.6 years ago shepherl 4.3k
1
vote
3
replies
3.6k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 120
0
votes
3
replies
2.5k
views
Analysing TCGA Level 3 Copy Number Data Location of markers in the genome
TCGA Cancer dnacopy segmentation
updated 8.7 years ago by ▴ 130 • written 8.7 years ago by • 0
0
votes
2
replies
4.1k
views
Error using TCGAbiolinks "Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column"
TCGA tcgabiolinks Error
8.7 years ago f.geist ▴ 20
2
votes
2
replies
2.0k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r tcga recount iranges
updated 8.7 years ago by ★ 1.1k • written 8.7 years ago by ▴ 20
1
vote
0
replies
2.5k
views
Problem about module preservation statistics in WGCNA software
rnaseq tcga wgcna
8.9 years ago • updated 8.8 years ago panagiotis.mokos ▴ 40
0
votes
2
replies
5.1k
views
Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 8.9 years ago by ▴ 260 • written 9.1 years ago by • 0
0
votes
0
replies
3.2k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
9.0 years ago • updated 8.9 years ago panagiotis.mokos ▴ 40
3
votes
12
replies
5.0k
views
Problem about use of TCGA rna-seq rsem gene results for regularized cox regression modeling
tcga rnaseq glmnet voom deseq2
9.0 years ago panagiotis.mokos ▴ 40
25
votes
37
replies
18k
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 9.1 years ago by 53k • written 9.1 years ago by ▴ 840
0
votes
1
reply
1.2k
views
TCGA Lung Cancer Pulmonary Function Test Data
tcga lusc luad pft pulmonary function test
9.2 years ago zyr123 • 0
1
vote
4
replies
2.8k
views
Error on creation of DESEq2 object
deseq2 tcga
updated 9.3 years ago by 43k • written 9.3 years ago by ▴ 40
0
votes
0
replies
1.5k
views
how to annotate TCGA snp6 data with genomic coordinates
microarray tcga annotation snp6.0
9.3 years ago seeker • 0
0
votes
4
replies
2.1k
views
TCGABiolinks not available for R3.3.0
TCGA tcgabiolinks R
updated 9.7 years ago by 25k • written 9.7 years ago by • 0
2
votes
6
replies
2.8k
views
Using TCGAbiolinks for exon and oligonucleotide level microarray
tcga tcgabiolinks microarray exons oligonucleotide
updated 9.8 years ago by ▴ 270 • written 9.8 years ago by • 0
0
votes
1
reply
1.8k
views
LuminalA Breast cancer subtype samples from GEO GSE62944
tcga cancer BreastCancer gse62944 luminalA
updated 9.9 years ago by ▴ 150 • written 9.9 years ago by • 0
0
votes
2
replies
1.7k
views
Differential gene expression analysis for GSE62944
R limma cancer tcga bioconductor
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by • 0
0
votes
0
replies
972
views
TCGAvisualize_EAbarplot Function Issues, won't produce expected charts
TCGA
10.0 years ago pgreylin • 0
0
votes
2
replies
2.2k
views
mutational signatures problems
bsgenome readvcf tcga annotation somaticsignatures
updated 17 months ago by • 0 • written 10.0 years ago by • 0
1
vote
3
replies
5.3k
views
R Text progress bar error
TCGA
10.2 years ago devyani66 • 0
0
votes
3
replies
2.1k
views
Mapping of two different regions to one gene symbol
TCGA CNV
updated 10.8 years ago by ★ 7.2k • written 10.8 years ago by ▴ 60
4
votes
3
replies
3.4k
views
DESeq2 - design for TCGA level 3 data
deseq2 tcga experimental design multiple factor design
updated 10.8 years ago by 43k • written 10.8 years ago by ▴ 40
0
votes
0
replies
980
views
RNAseq binary transformation
tcga binary rnaseq
10.8 years ago ezz • 0
1
vote
4
replies
4.0k
views
Different clustering results of DESeq2 counts and rlog
tcga nomalization rnaseq deseq2
10.8 years ago ezz • 0
0
votes
2
replies
4.0k
views
Pipeline for analyzing CNV (SNP array) level 3 from TCGA
SNP CNV TCGA
10.8 years ago NS ▴ 60
105 results • Page 2 of 3
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Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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