Showing : GenomicDataCommons • reset
5
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11
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3.9k
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Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 4.8 years ago by 690 • written 4.8 years ago by ★ 1.5k
0
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4
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2.2k
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extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons R
updated 2.7 years ago by ▴ 50 • written 4.2 years ago by ▴ 40
4
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4
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1.2k
views
2 questions: why there is nothing for file_ids? How could I generate a manifest file with filtering of Race and Ethnicity?
GenomicDataCommons
2.7 years ago xiaofeiwang18266 ▴ 50
4
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2
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1.1k
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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
3
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2
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1.1k
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How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 2.4 years ago by ★ 3.3k • written 2.4 years ago by ▴ 10
0
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1
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800
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Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
3.1 years ago Ezgi ▴ 60
0
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1
reply
498
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GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 10 months ago by ▴ 490
0
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1
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382
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Why 3 RNA-seq bams for same sample/aliquot_barcode?
manifest GDCdownload GenomicDataCommons
8 months ago xiaofeiwang198266 • 0
8 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
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Supporter to Jonathan ▴ 10
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