Showing : TCGAbiolinks • reset
0
votes
1
reply
63
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 26 days ago by 34k • written 27 days ago by • 0
0
votes
7
replies
1.6k
views
GDCquery(project = "TCGA-COAD") did not work; but GDCquery(project = "TCGA-READ") workl why???
gdcquery tcgabiolinks
updated 5 weeks ago by • 0 • written 3.3 years ago by • 0
0
votes
0
replies
60
views
DEGs for legacy and harmonized dataset
#DEGs #legacydataset #harmonizeddataset TCGAbiolinks
updated 6 weeks ago by 3.4k • written 6 weeks ago by • 0
0
votes
1
reply
101
views
Help With TCGAbiolinks package
TCGAbiolinks data normalize l
updated 7 weeks ago by 3.4k • written 7 weeks ago by • 0
0
votes
2
replies
155
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
3 months ago H. Z. Amini • 0
0
votes
0
replies
143
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
3 months ago H. Z. Amini • 0
0
votes
0
replies
97
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
4 months ago rebeliscu • 0
0
votes
3
replies
198
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
5 months ago xiaofeiwang18266 ▴ 40
1
vote
1
reply
224
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 5 months ago by 34k • written 5 months ago by ▴ 40
3
votes
8
replies
597
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
5 months ago xiaofeiwang18266 ▴ 40
0
votes
0
replies
154
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
5 months ago martin.schaefer • 0
0
votes
1
reply
164
views
library(TCGAbiolinks)
TCGAbiolinks
updated 7 months ago by 3.4k • written 7 months ago by • 0
3
votes
7
replies
2.5k
views
how to add a new column in colData in SummarizedExperiment
summarizedexperiment tcgabiolinks
written 3.3 years ago by • 0
0
votes
1
reply
204
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
8 months ago • updated 7 months ago Sophie Marion de Proce • 0
0
votes
1
reply
179
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 9 months ago by 2.8k • written 9 months ago by • 0
0
votes
3
replies
264
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
12 months ago aush ▴ 40
0
votes
5
replies
300
views
TCGA: to extract clinical data from barcode
cancer TCGAbiolinks
updated 12 months ago by 3.4k • written 12 months ago by ▴ 10
0
votes
5
replies
287
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 12 months ago by ▴ 260 • written 12 months ago by ▴ 40
4
votes
6
replies
328
views
TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
13 months ago mario.zanfardino ▴ 160
0
votes
4
replies
248
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks R.oo
updated 14 months ago by 58k • written 14 months ago by ▴ 10
0
votes
2
replies
676
views
TCGAbiolinks BioMart error
TCGAbiolinks BioMart
updated 14 months ago by 58k • written 14 months ago by ▴ 10
1
vote
3
replies
722
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation permission denied RTCGAToolbox TCGAbiolinks
16 months ago julia.tutzauer • 0
0
votes
0
replies
171
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
20 months ago jam526 • 0
0
votes
1
reply
784
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
20 months ago ph.shimaasherif • 0
0
votes
0
replies
293
views
Error in downloading the MAF file for the TARGET data
TCGAbiolinks TARGET MAF
21 months ago ph.shimaasherif • 0
2
votes
4
replies
317
views
Error : Results must have the same dimensions
TCGAbiolinks GDC dataset
21 months ago ph.shimaasherif • 0
0
votes
0
replies
188
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
21 months ago modarzi ▴ 10
0
votes
4
replies
314
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
21 months ago modarzi ▴ 10
1
vote
3
replies
410
views
Missing Clinical LIHC Data
Missing Data TCGAbiolinks Kaplan-Meier LIHC Xenabrowser
22 months ago jam526 • 0
0
votes
0
replies
359
views
GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
23 months ago fawazfebin ▴ 30
0
votes
1
reply
257
views
error reading from connection
TCGAbiolinks
updated 5 months ago by 3.4k • written 23 months ago by • 0
5
votes
11
replies
1.3k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 2.2 years ago by 550 • written 2.2 years ago by ★ 1.5k
4
votes
5
replies
817
views
GDCprepare - error
TCGABiolinks GDCprepare
2.2 years ago vm • 0
2
votes
2
replies
610
views
TCGAbiolinks GDCprepare error
TCGAbiolinks GDCprepare error
updated 2.2 years ago by ▴ 150 • written 2.2 years ago by ▴ 10
1
vote
2
replies
279
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 2.2 years ago by ▴ 260 • written 2.2 years ago by • 0
0
votes
1
reply
530
views
Downloading HTSeq raw reads with TCGABiolinks
TCGAbiolinks RNASEQ
2.3 years ago • updated 2.2 years ago sherajilir • 0
2
votes
4
replies
533
views
Missing clinical data at TCGAbiolinks data
TCGAbiolinks days_to_death clinical data missing column
updated 2.4 years ago by ▴ 260 • written 2.4 years ago by ▴ 10
0
votes
0
replies
295
views
GDCdownload error on CentOS 6.10 server
TCGAbiolinks
2.4 years ago t.kuilman 170
0
votes
0
replies
425
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
2.5 years ago gerald.mccollam • 0
0
votes
0
replies
304
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
2.5 years ago Yonatan Amzaleg • 0
1
vote
3
replies
447
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 2.5 years ago by ▴ 260 • written 2.5 years ago by ▴ 10
2
votes
5
replies
1.2k
views
GDCdownload does not work
GDCdow tcgabiolinks error tcgadownload download_error
updated 2.8 years ago by ▴ 260 • written 2.8 years ago by • 0
0
votes
2
replies
713
views
GDCprepare stop working for some unknown reason
tcgabiolinks gdcprepare
updated 2.8 years ago by 58k • written 2.8 years ago by • 0
3
votes
1
reply
697
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.8 years ago by ★ 1.5k • written 2.8 years ago by ▴ 10
0
votes
2
replies
924
views
Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
tcgabiolinks dplyr DT
3.0 years ago Mithil Gaikwad • 0
0
votes
2
replies
924
views
GDC server down, try to use this package later
tcgabiolinks
3.0 years ago Mithil Gaikwad • 0
0
votes
0
replies
415
views
Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
3.0 years ago mtkk94 • 0
2
votes
5
replies
698
views
TCGAbiolinksGUI is not stable on windows 7.
tcgabiolinks tcgabiolinksgui
updated 3.1 years ago by ▴ 10 • written 3.1 years ago by • 0
4
votes
1
reply
12k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
3.1 years ago ansari.sarabio • 0
3
votes
4
replies
946
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
3.1 years ago franceschini.gianmarco • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Volcano plots of DEGs from Swish are weird by Qin ▴ 10
Thans for your reply. I'm sorry for reply so late, because I didn't getting any messages in my email. I will read details of the vignette.
Comment: At least one covariate is confounded with batch! Please remove confounded covari by NewBioInfo • 0
Thank you, James. I was indeed using the wrong matrix. The `nonExtimable` did give me the column name which was causing the issue but I do …
Comment: Returning to edgeR version 3.26.1? by Gordon Smyth 43k
I don't think that any changes to edgeR between 3.26.1 and 3.26.8 could have caused the changes that you show.
Comment: Returning to edgeR version 3.26.1? by mvanhorn • 0
Thank you very much for your reply! Our project is a reanalysis of large sets of RNA-seq data to identify circular RNAs using the CIRIquan…
Comment: "full model matrix is less than full rank" by ATpoint ▴ 840
My best guess is that young and old are not "young" or "old" but include some hidden whitespaces like " young" or "old ". That would then m…
Votes
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: Swish direction of comparison based on order of factors
Comment: Gradient dotplot
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Awards • All
Scholar to Gordon Smyth 43k
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Hans-Ulrich Klein ▴ 330
Popular Question to Hervé Pagès 15k
Scholar to Jiang, Mike ★ 1.3k
Locations • All
Novartis Institutes for BioMedical Research, 5 minutes ago
WEHI, Melbourne, Australia, 13 minutes ago
Switzerland, 31 minutes ago
San Diego, 31 minutes ago
Spain, 34 minutes ago
Traffic: 249 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