Showing : gdc • reset
0
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2
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3.7k
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Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 7.1 years ago by ▴ 260 • written 7.2 years ago by • 0
0
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11
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3.2k
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TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
7.5 years ago • updated 7.4 years ago jshelton • 0
17
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8
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3.1k
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How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 6.0 years ago by 21k • written 6.0 years ago by ▴ 110
0
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1
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3.0k
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how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks tcga-brca gdc pam50 rna-seq
6.1 years ago pfrancislyon • 0
3
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2
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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
7
votes
7
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1.6k
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Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 5.5 years ago by 21k • written 5.5 years ago by ▴ 50
1
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2
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1.3k
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 5.0 years ago by 21k • written 5.0 years ago by ▴ 160
0
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4
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1.2k
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problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
4.4 years ago modarzi ▴ 10
4
votes
2
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1.1k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 5.3 years ago by 21k • written 5.3 years ago by ▴ 20
0
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0
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974
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Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
4.3 years ago jam526 • 0
0
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0
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709
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
4.4 years ago modarzi ▴ 10
0
votes
1
reply
497
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 10 months ago by ▴ 490
12 results • Page 1 of 1
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Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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