Showing : tcgabiolinks • reset
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 5 weeks ago by ▴ 20 • written 6.6 years ago by ▴ 100
0
votes
1
reply
218
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 6 weeks ago by • 0
0
votes
0
replies
141
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
7 weeks ago • updated 5 weeks ago Giovanni Calice ▴ 160
1
vote
0
replies
160
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
8 weeks ago BioinfoMug • 0
0
votes
0
replies
158
views
GDC slides download
TCGAbiolinks
10 weeks ago jain72744 • 0
0
votes
4
replies
280
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks Survival
updated 10 weeks ago by ▴ 730 • written 10 weeks ago by • 0
0
votes
0
replies
147
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
12 weeks ago Thalita • 0
0
votes
1
reply
388
views
Problems when running GDC_prepare in R
TCGAbiolinks error GDC_prepare
6 months ago leon • 0
0
votes
0
replies
246
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical TCGAbiolinks
9 months ago BioInfoBeginnerrr • 0
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago • updated 10 months ago Habil Zare ▴ 200
0
votes
2
replies
850
views
RPPA data (Proteomics analysis)
TCGAbiolinks limma
13 months ago • updated 12 months ago qiz218591 • 0
1
vote
1
reply
759
views
Error when running getGDCprojects()
TCGAbiolinks
13 months ago DevelopingHippo • 0
0
votes
1
reply
616
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
540
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
14 months ago DevelopingHippo • 0
1
vote
3
replies
937
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
15 months ago Alexandre • 0
0
votes
0
replies
460
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
18 months ago lescano ▴ 10
0
votes
0
replies
637
views
Query on TCGA
TCGAbiolinks TCGAWorkflow
20 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
719
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
21 months ago qiz218591 • 0
0
votes
0
replies
518
views
TCGAbiolinks file.type argument
TCGAbiolinks
21 months ago Elizabeth • 0
0
votes
0
replies
538
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
23 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
983
views
GDCdownload Directory Problem :(
TCGAWorkflowData TCGAbiolinks
updated 9 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 2.0 years ago by ▴ 270 • written 2.0 years ago by • 0
0
votes
1
reply
1.9k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 19 months ago by • 0 • written 2.0 years 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 2.0 years ago by • 0 • written 3.6 years ago by ▴ 40
0
votes
0
replies
570
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.1 years ago komal.rathi ▴ 120
0
votes
2
replies
2.1k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
2.1 years ago • updated 19 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
802
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.4 years ago constantinosdem • 0
0
votes
0
replies
668
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
2.5 years ago raf4 ▴ 20
1
vote
2
replies
1.0k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
2.5 years ago raf4 ▴ 20
0
votes
1
reply
1.3k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
votes
0
replies
709
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
1.6k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
2.9 years ago H. Z. Amini ▴ 10
0
votes
0
replies
727
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
3.0 years ago rebeliscu • 0
0
votes
3
replies
933
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
3.0 years ago xiaofeiwang18266 ▴ 50
1
vote
1
reply
1.4k
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
3.5k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
3.1 years ago • updated 3.0 years ago xiaofeiwang18266 ▴ 50
0
votes
0
replies
845
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
806
views
library(TCGAbiolinks)
TCGAbiolinks
updated 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 0
0
votes
1
reply
1.7k
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
902
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 3.4 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: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
Awards • All
Popular Question to Leo Lahti ▴ 40
Scholar to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Scholar to Michael Love 41k
Supporter to JKim • 0
Locations • All
WEHI, Melbourne, Australia, 17 minutes ago
Ireland, 50 minutes ago
France, 1 hour ago
United States, 1 hour ago
Belgium, 2 hours ago
Traffic: 575 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