Showing : tcga • reset
0
votes
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206
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 5 weeks ago by • 0
1
vote
0
replies
146
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
7 weeks ago BioinfoMug • 0
7
votes
18
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2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 3 months ago by ▴ 240 • written 7.0 years ago by ▴ 20
0
votes
2
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511
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 5 months ago by ★ 1.0k • written 5 months ago by ▴ 190
0
votes
1
reply
491
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 9 months ago by ▴ 490
1
vote
1
reply
477
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 9 months ago by ★ 4.0k • written 9 months ago by • 0
1
vote
3
replies
982
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 11 months ago by ★ 4.0k • written 11 months ago by ▴ 20
0
votes
1
reply
613
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 16 months ago by ★ 4.0k • written 16 months ago by • 0
2
votes
9
replies
2.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
22 months ago Peipei • 0
2
votes
2
replies
1.9k
views
Create TPM gene tables/dataframe from ReCount3
recount3 TCGA GTEx DESeq2
22 months ago David ▴ 20
3
votes
2
replies
2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.0 years ago by • 0 • written 5.4 years ago by ▴ 10
2
votes
5
replies
1.5k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 24 months ago by • 0 • written 3.6 years ago by ▴ 40
1
vote
1
reply
1.0k
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 2.1 years ago by ★ 1.0k • written 2.1 years ago by ▴ 10
0
votes
2
replies
860
views
Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
2.2 years ago IamFrofro • 0
3
votes
2
replies
1.1k
views
How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 2.4 years ago by ★ 3.2k • written 2.4 years ago by ▴ 10
5
votes
9
replies
3.2k
views
Error via running GDCquey from TCGAbiolinks package
TCGA Genome Data Common portal
updated 2.9 years ago by ▴ 10 • written 5.8 years ago by ▴ 10
0
votes
0
replies
717
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
2.9 years ago rebeliscu • 0
0
votes
1
reply
794
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
3.1 years ago Ezgi ▴ 60
0
votes
0
replies
945
views
Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
3.5 years ago Laurent Gatto 1.6k
0
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0
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712
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
3.6 years ago andrade4beatriz • 0
0
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5
replies
2.7k
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 3.6 years ago by ▴ 260 • written 3.6 years ago by ▴ 40
4
votes
7
replies
3.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 0
0
votes
2
replies
1.4k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 4.1 years ago by ★ 1.0k • written 4.1 years ago by • 0
4
votes
7
replies
1.1k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 60
0
votes
0
replies
703
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
4.4 years ago modarzi ▴ 10
0
votes
4
replies
1.2k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
4.4 years ago modarzi ▴ 10
2
votes
3
replies
794
views
DESeq2 doesn't return the most drastically DEG
deseq2 tcga
4.5 years ago ndjayne • 0
2
votes
2
replies
2.2k
views
DESeq2: design = ~1 For Normalisation Only.
deseq2 limma normalization tcga rnaseq
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
1
vote
2
replies
1.1k
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 4.8 years ago by ▴ 260 • written 4.8 years ago by • 0
1
vote
1
reply
1.2k
views
TCGA isoform expression quantification file - how to reshape data
data.frame tcga reshape data
updated 4.9 years ago by ★ 13k • written 4.9 years ago by ▴ 160
1
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2
replies
1.3k
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 4.9 years ago by 21k • written 5.0 years ago by ▴ 160
0
votes
1
reply
1.1k
views
How to download the TCGA SKCM subtype information?
TCGA melanoma TCGA SKCM
5.0 years ago syrttgump ▴ 20
5
votes
4
replies
1.8k
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 5.0 years ago by ★ 1.1k • written 5.0 years ago by ▴ 830
0
votes
0
replies
958
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
5.1 years ago Yonatan Amzaleg • 0
1
vote
3
replies
2.0k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 5.1 years ago by ▴ 260 • written 5.1 years ago by ▴ 10
4
votes
6
replies
3.5k
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 5.2 years ago by 41k • written 5.2 years ago by ▴ 70
1
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5
replies
1.6k
views
Issue with TCGAbiolinks package.
TCGA GDCprepare
5.2 years ago salvocomplicazioni1 • 0
0
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0
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804
views
Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation reference CNA TCGA
5.2 years ago jlarsen728 • 0
4
votes
2
replies
1.1k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 5.2 years ago by 21k • written 5.2 years ago by ▴ 20
0
votes
0
replies
1.0k
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA geneset RNASeq TCGA subtypes
5.3 years ago Pietro ▴ 40
0
votes
0
replies
898
views
GDC RNA seq files (replicates?)
gdc data TCGA gdcdownload
5.3 years ago coyoung ▴ 10
2
votes
4
replies
1.3k
views
edgeR. Known cancer genes are not differentially expressed?
edger tcga
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
0
votes
1
reply
1.1k
views
RNAseq gene expression analysis in Personalized genomics
TCGA deseq2 edger limma
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
2
votes
3
replies
1.4k
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package TCGA LocusLinkID genecode ensembl
updated 5.5 years ago by 65k • written 5.5 years ago by ▴ 10
8
votes
12
replies
6.1k
views
MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
multiassayexperiment wide format TCGA
updated 5.6 years ago by 690 • written 5.6 years ago by ▴ 160
8
votes
8
replies
6.7k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 5.6 years ago by ★ 7.9k • written 5.6 years ago by ▴ 60
1
vote
2
replies
1.2k
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 5.6 years ago by 50k • written 5.6 years ago by • 0
3
votes
4
replies
2.3k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
5.7 years ago franceschini.gianmarco • 0
0
votes
5
replies
2.1k
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 5.7 years ago by ▴ 270 • written 5.7 years ago by ▴ 60
4
votes
2
replies
2.0k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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Scholar to Robert Castelo ★ 3.2k
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