Showing : TCGABiolinks • reset
1
vote
3
replies
3.0k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 4 weeks ago by ▴ 20 • written 6.5 years ago by ▴ 100
0
votes
1
reply
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
0
votes
0
replies
133
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
6 weeks ago • updated 4 weeks ago Giovanni Calice ▴ 160
1
vote
0
replies
144
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
7 weeks ago BioinfoMug • 0
0
votes
0
replies
139
views
GDC slides download
TCGAbiolinks
9 weeks ago jain72744 • 0
0
votes
4
replies
259
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks Survival
updated 9 weeks ago by ▴ 730 • written 9 weeks ago by • 0
0
votes
0
replies
139
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
11 weeks ago Thalita • 0
0
votes
1
reply
370
views
Problems when running GDC_prepare in R
TCGAbiolinks error GDC_prepare
5 months ago leon • 0
0
votes
0
replies
239
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical TCGAbiolinks
9 months ago BioInfoBeginnerrr • 0
4
votes
8
replies
1.1k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago • updated 10 months ago Habil Zare ▴ 200
0
votes
2
replies
835
views
RPPA data (Proteomics analysis)
TCGAbiolinks limma
12 months ago • updated 11 months ago qiz218591 • 0
1
vote
1
reply
748
views
Error when running getGDCprojects()
TCGAbiolinks
13 months ago DevelopingHippo • 0
0
votes
1
reply
601
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 8 months ago by • 0 • written 13 months ago by ▴ 20
0
votes
0
replies
522
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
13 months ago Manav • 0
1
vote
2
replies
1.5k
views
Error when running GDC_prepare
TCGAbiolinks
13 months ago DevelopingHippo • 0
1
vote
3
replies
915
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
15 months ago Alexandre • 0
0
votes
0
replies
451
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
17 months ago lescano ▴ 10
0
votes
0
replies
620
views
Query on TCGA
TCGAbiolinks TCGAWorkflow
19 months ago hemangininaik09 • 0
0
votes
2
replies
1.3k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 20 months ago by ▴ 270 • written 22 months ago by • 0
0
votes
0
replies
709
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
21 months ago qiz218591 • 0
0
votes
0
replies
509
views
TCGAbiolinks file.type argument
TCGAbiolinks
21 months ago Elizabeth • 0
0
votes
0
replies
530
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
22 months ago syednajeebashraf • 0
5
votes
4
replies
2.8k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 23 months ago by ★ 1.3k • written 2.1 years ago by ▴ 30
0
votes
4
replies
960
views
GDCdownload Directory Problem :(
TCGAWorkflowData TCGAbiolinks
updated 8 weeks ago by 690 • written 24 months ago by • 0
0
votes
2
replies
2.1k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks TARGET-AML
updated 24 months ago by ▴ 270 • written 2.0 years ago by • 0
0
votes
1
reply
1.8k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 19 months ago by • 0 • written 24 months ago by • 0
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
0
votes
0
replies
554
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.0 years ago komal.rathi ▴ 120
0
votes
2
replies
2.1k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
2.0 years ago • updated 18 months ago spyrouglykeria • 0
6
votes
3
replies
3.1k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.0 years ago by • 0 • written 2.1 years ago by ▴ 10
2
votes
8
replies
4.8k
views
GDCquery_Maf error
TCGAbiolinks GDCquery_Maf
updated 21 months ago by • 0 • written 2.1 years ago by • 0
0
votes
0
replies
793
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.3 years ago constantinosdem • 0
0
votes
0
replies
658
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq TCGAbiolinks TCGAAnalyze_DEA
2.4 years ago Gandino • 0
0
votes
1
reply
2.1k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
2.4 years ago raf4 ▴ 20
1
vote
2
replies
1.0k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
2.5 years ago • updated 2.4 years ago raf4 ▴ 20
0
votes
1
reply
1.3k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 2.6 years ago by 41k • written 2.7 years ago by • 0
0
votes
0
replies
695
views
DEGs for legacy and harmonized dataset
#DEGs #legacydataset #harmonizeddataset TCGAbiolinks
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
Help With TCGAbiolinks package
TCGAbiolinks data normalize l
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
votes
2
replies
1.1k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
2.9 years ago H. Z. Amini ▴ 10
0
votes
0
replies
1.5k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
2.9 years ago H. Z. Amini ▴ 10
0
votes
0
replies
716
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
2.9 years ago rebeliscu • 0
0
votes
3
replies
922
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
3.0 years ago xiaofeiwang18266 ▴ 50
1
vote
1
reply
1.3k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 3.0 years ago by 41k • written 3.0 years ago by ▴ 50
3
votes
8
replies
3.4k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
3.0 years ago xiaofeiwang18266 ▴ 50
0
votes
0
replies
841
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
3.1 years ago martin.schaefer • 0
0
votes
1
reply
800
views
library(TCGAbiolinks)
TCGAbiolinks
updated 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 0
0
votes
1
reply
1.6k
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
3.3 years ago • updated 3.2 years ago Sophie Marion de Proce • 0
0
votes
1
reply
889
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 3.3 years ago by 3.8k • written 3.4 years ago by • 0
0
votes
5
replies
2.0k
views
TCGA: to extract clinical data from barcode
cancer TCGAbiolinks
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
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…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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
Awards • All
Popular Question to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Popular Question to BioinfGuru ▴ 30
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Locations • All
United States, 24 minutes ago
France, 29 minutes ago
WEHI, Melbourne, Australia, 36 minutes ago
Vietnam, 49 minutes ago
United States, 1 hour ago
Traffic: 498 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6