Showing : tcga • reset
5
votes
9
replies
1.1k
views
Error via running GDCquey from TCGAbiolinks package
TCGA Genome Data Common portal
updated 8 weeks ago by • 0 • written 3.1 years ago by ▴ 10
0
votes
0
replies
68
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
10 weeks ago rebeliscu • 0
0
votes
1
reply
87
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
4 months ago Ezgi ▴ 30
0
votes
0
replies
216
views
Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
9 months ago Laurent Gatto 1.5k
0
votes
3
replies
215
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
10 months ago aush ▴ 40
0
votes
0
replies
141
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
10 months ago andrade4beatriz • 0
0
votes
5
replies
244
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 11 months ago by ▴ 260 • written 11 months ago by ▴ 40
7
votes
17
replies
1.1k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 12 months ago by ▴ 220 • written 4.3 years ago by ▴ 20
4
votes
7
replies
640
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 14 months ago by 3.2k • written 14 months ago by • 0
0
votes
2
replies
221
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 16 months ago by ▴ 890 • written 17 months ago by • 0
4
votes
7
replies
179
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 16 months ago by 57k • written 16 months ago by ▴ 30
0
votes
0
replies
167
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
19 months ago modarzi ▴ 10
0
votes
4
replies
275
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
20 months ago modarzi ▴ 10
2
votes
3
replies
219
views
DESeq2 doesn't return the most drastically DEG
deseq2 tcga
21 months ago ndjayne • 0
2
votes
2
replies
246
views
DESeq2: design = ~1 For Normalisation Only.
deseq2 limma normalization tcga rnaseq
updated 21 months ago by 33k • written 21 months ago by • 0
1
vote
2
replies
247
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 2.1 years ago by ▴ 260 • written 2.1 years ago by • 0
1
vote
1
reply
308
views
TCGA isoform expression quantification file - how to reshape data
data.frame tcga reshape data
updated 2.2 years ago by 13k • written 2.2 years ago by ▴ 160
1
vote
2
replies
349
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 2.2 years ago by 21k • written 2.2 years ago by ▴ 160
0
votes
1
reply
270
views
How to download the TCGA SKCM subtype information?
TCGA melanoma TCGA SKCM
2.2 years ago syrttgump ▴ 20
4
votes
4
replies
521
views
Perform correlation analysis between miRNA and mRNA gene expression data on the same TCGA dataset based on the curatedTCGAData
curatedTCGAData MultiAssayExperiment multiomics TCGA
updated 2.3 years ago by 1.1k • written 2.3 years ago by ▴ 780
0
votes
0
replies
273
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
2.4 years ago Yonatan Amzaleg • 0
1
vote
3
replies
412
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 2.4 years ago by ▴ 260 • written 2.4 years ago by ▴ 10
4
votes
6
replies
1.7k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2 normalization rna-seq TCGA vst
updated 2.4 years ago by 33k • written 2.4 years ago by ▴ 70
1
vote
5
replies
474
views
Issue with TCGAbiolinks package.
TCGA GDCprepare
2.5 years ago salvocomplicazioni1 • 0
0
votes
0
replies
245
views
Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation reference CNA TCGA
2.5 years ago jlarsen728 • 0
4
votes
2
replies
392
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 2.5 years ago by 21k • written 2.5 years ago by ▴ 20
0
votes
0
replies
445
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA geneset RNASeq TCGA subtypes
2.6 years ago Pietro ▴ 30
0
votes
0
replies
277
views
GDC RNA seq files (replicates?)
gdc data TCGA gdcdownload
2.6 years ago coyoung ▴ 10
2
votes
4
replies
468
views
edgeR. Known cancer genes are not differentially expressed?
edger tcga
updated 2.6 years ago by ★ 27k • written 2.6 years ago by ▴ 20
3
votes
1
reply
651
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.7 years ago by ★ 1.5k • written 2.7 years ago by ▴ 10
0
votes
1
reply
410
views
RNAseq gene expression analysis in Personalized genomics
TCGA deseq2 edger limma
updated 2.7 years ago by 33k • written 2.7 years ago by • 0
2
votes
3
replies
549
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package TCGA LocusLinkID genecode ensembl
updated 2.8 years ago by 57k • written 2.8 years ago by ▴ 10
8
votes
12
replies
946
views
MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
multiassayexperiment wide format TCGA
updated 2.8 years ago by 540 • written 2.8 years ago by ▴ 160
8
votes
8
replies
2.7k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 2.8 years ago by 7.6k • written 2.8 years ago by ▴ 50
1
vote
2
replies
433
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2 edger fpkm counts TCGA
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
3
votes
4
replies
884
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
2.9 years ago franceschini.gianmarco • 0
0
votes
5
replies
778
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 2.9 years ago by ▴ 240 • written 2.9 years ago by ▴ 50
4
votes
2
replies
827
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 3.0 years ago by 13k • written 3.0 years ago by ▴ 50
0
votes
2
replies
1.5k
views
Error: vector memory exhausted (limit reached?)
tcgabiolinks tcga cnv mac os x gaia
updated 3.0 years ago by ▴ 20 • written 3.0 years ago by ▴ 20
6
votes
7
replies
673
views
Download TCGA dataset like a S4 object
dataset tcga
updated 3.0 years ago by ▴ 160 • written 3.0 years ago by ▴ 20
0
votes
0
replies
367
views
Noise Analyses of CNV Data from TCGA
tcgabiolinks tcga cnv noise pruning
3.1 years ago jrlarsen ▴ 10
8
votes
5
replies
748
views
Querying specific TCGA datasets through the MultiAssayExperiment R package
MultiAssayExperiment curatedCRCdata multiomics TCGA
updated 3.1 years ago by 540 • written 3.1 years ago by ▴ 780
2
votes
1
reply
1.0k
views
Error in TCGAquery of TCGAbiolinks Package
software error bioconductor tcgabiolinks tcga r
updated 3.2 years ago by ▴ 90 • written 3.2 years ago by ▴ 50
0
votes
0
replies
554
views
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
deseq2 tcga
updated 3.2 years ago by 33k • written 3.2 years ago by • 0
3
votes
3
replies
594
views
Retrieve accurate tumor stage data with TCGAbiolinks
tcgabiolinks tcga
3.2 years ago Benjamin Ostendorf ▴ 90
17
votes
8
replies
1.4k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 90
6
votes
14
replies
1.3k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by ▴ 20
0
votes
2
replies
2.7k
views
Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 3.3 years ago by • 0 • written 6.3 years ago by • 0
3
votes
2
replies
402
views
Can i add an experiment to an existing MultiAssayExperiment?
mutiassayexperiment tcga tcia
3.4 years ago mario.zanfardino ▴ 160
0
votes
2
replies
468
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount metadata tcga
updated 3.4 years ago by • 0 • written 3.4 years ago by • 0
50 results • Page 1 of 1
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Answer: How to extract DEG from limmarResults object after beadarray analysis by Gordon Smyth 43k
I am the limma package author, but I don't know how to help you. The beadarray package has done a standard limma analysis but, instead of s…
Comment: An error using Diffbind plotprofile by doug.barrows • 0
Hi there, it's hard to tell how to debug without having the data. Could you potentially send me the object you are attempting to use for th…
Comment: DESeq2 Shrinkage methods for scRNA-Seq by Pedro Tan • 0
Thanks Michael! I will stick to apeglm and incorporate alternate size factors for single cell data. All the best, Pedro
Answer: Macbook M1 install genefilter failed by soda ▴ 10
i have solved this problem by myself. share with you. you need to download gfortran in path /opt/R/arm64/bin this website helped me: **h…
Comment: Best practice for quantifying sncRNA by James W. MacDonald 57k
If you used the QIASeq miRNA library, then you are wasting your time. That library adds the UMI barcodes and is intended for you to then up…
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Answer: Macbook M1 install genefilter failed
BioCAsia Virtual Meeting, 15-18 October 2020
Answer: Selecting pairs of exons from differentially spliced genes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
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