User: Sheldon Pang

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Sheldon Pang20
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Posts by Sheldon Pang

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recount TCGA data one gene_id mapped to multiple symbols and vice versa
... For example: Gene id ENSG00000283638 mapped to multiple symbols MIR106A MIR19B2 MIR92A2 MIR363 MIR20B MIR18B Gene id ENSG00000015479 and ENSG00000280987 both mapped to symbol MATR3 It looks to me these are incorrect. Any idea? Thanks. > library(recount) > recount_genes$symbol[57992] \# Chara ...
recount written 4 weeks ago by Sheldon Pang20 • updated 4 weeks ago by Leonardo Collado Torres710
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Number of reads from recount are greater than target library size (40 million) for TCGA and GTEx projects
... I just quickly check the data from TCGA project and found that some number of reads are greater than the target library size 40 million. Any ideas? Similarly for GTEx too. The code is as follows: library("recount") accession = "TCGA" download_study(accession, type = "rse-gene") load(fi ...
recount written 8 months ago by Sheldon Pang20 • updated 8 months ago by Leonardo Collado Torres710

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