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Why 3 RNA-seq bams for same sample/aliquot_barcode?
manifest GDCdownload GenomicDataCommons
16 months ago xiaofeiwang198266 • 0
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740
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GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 17 months ago by ▴ 510
3
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2
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1.3k
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How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 3.0 years ago by ★ 3.4k • written 3.0 years ago by ▴ 10
4
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4
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1.6k
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2 questions: why there is nothing for file_ids? How could I generate a manifest file with filtering of Race and Ethnicity?
GenomicDataCommons
3.3 years ago xiaofeiwang18266 ▴ 50
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1.0k
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Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
3.7 years ago Ezgi ▴ 60
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4
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2.8k
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extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons R
updated 3.3 years ago by ▴ 50 • written 4.8 years ago by ▴ 40
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11
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4.6k
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Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 5.4 years ago by 700 • written 5.4 years ago by ★ 1.5k
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GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 5.8 years ago by 21k • written 5.9 years ago by ▴ 20
8 results • Page 1 of 1
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Comment: Create Illmina bead summary data by Liu • 0
Hi! Yes, thank you! I completely agree. I am just curious about how these two files are processed with AVG_Gre and detection p-value. I am …
Answer: Epic v2 Annotation CpG_maf source? by James W. MacDonald 67k
Those all come from dbSNP by way of UCSC. [See here][1], particularly lines 114 and onward. Here is no MAF for a CpG. The MAF is for the…
Comment: Deseq2 res Function by James W. MacDonald 67k
In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…
Answer: Struggle with the replicates of epic array data by James W. MacDonald 67k
You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …
Comment: Identifying potentially associated gene set to drug response using GSVA by Robert Castelo ★ 3.4k
So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…
Votes
Appropriate use of the function treat of the limma package
Comment: Is it recommended to analyze different tissues together when using edgeR
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
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