Showing : GDC • reset
17
votes
8
replies
1.8k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 90
7
votes
7
replies
854
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 3.6 years ago by 21k • written 3.6 years ago by ▴ 40
4
votes
2
replies
534
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 20
3
votes
2
replies
923
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 4 weeks ago by • 0 • written 3.5 years ago by ▴ 10
1
vote
2
replies
584
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 3.0 years ago by 21k • written 3.0 years ago by ▴ 160
0
votes
11
replies
2.1k
views
TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
5.5 years ago jshelton • 0
0
votes
0
replies
281
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
2.3 years ago jam526 • 0
0
votes
2
replies
2.7k
views
Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 5.1 years ago by ▴ 260 • written 5.3 years ago by • 0
0
votes
1
reply
2.0k
views
how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks tcga-brca gdc pam50 rna-seq
4.1 years ago pfrancislyon • 0
0
votes
4
replies
454
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
2.5 years ago modarzi ▴ 10
0
votes
0
replies
302
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
2.4 years ago modarzi ▴ 10
11 results • Page 1 of 1
Recent ...
Replies
Answer: Using featureCounts and downloading Rsubread by James W. MacDonald 59k
You need to tell `BiocManager;;install` that you want to install the `Rsubread` package. ``` BiocManager::install("Rsubread") library(…
Comment: featureCounts: 0% successfully assigned fragments by KMS • 0
Dear ATpoint I am exactly looking for read/gene count from BAM/SAM file either through ht-seq or feature count feature count giving me 0% s…
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene by James W. MacDonald 59k
There is the ncbiRefSeqSelect table that has the MANE and RefSeq Select transcripts. It's not just the MANE though. ``` > z <- makeTxDb…
Comment: Handling of missing values in limma by AyHi • 0
Thank you, Gordon, for your reply. I used sum(is.na(lmfit)) after lmFit, but somewhat it indicated there was no NA observations even when…
Comment: merging VCF files by lesefo6448 • 0
You can use this VCF Merger Software if you want to Merge VCF files into one file. this Software easily Merge your multiple VCF files with…
Votes
Answer: Load packages when using BatchtoolsParam
Comment: Load packages when using BatchtoolsParam
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
A: DESeq2: thousands of NA for pvalues?
Awards • All
Scholar to James W. MacDonald 59k
Popular Question to Gyan Prakash Mishra • 0
Scholar to ATpoint ★ 1.2k
Teacher to Gordon Smyth 45k
Scholar to Matthew McCormack ▴ 180
Locations • All
Israel, just now
United Kingdom, 11 minutes ago
France, 19 minutes ago
United States, 25 minutes ago
United States, 26 minutes ago
Traffic: 555 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