Bioconductor Tcgaworkflow

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TCGAWorkflow

11 weeks ago sameerahmadguru • 0

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TCGAWorkflow

12 months ago Begin-R • 0

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TCGAWorkflow

updated 19 months ago by ATpoint ★ 4.0k • written 19 months ago by fatemehfakhari74 • 0

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TCGAbiolinks TCGAWorkflow

19 months ago hemangininaik09 • 0

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DifferentialExpression TCGAWorkflow

2.5 years ago • updated 2.4 years ago Sam ▴ 10

5 results • Page 1 of 1

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Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0

0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…

Comment: Finding DEGs by using edgeR by Gordon Smyth 50k

Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …

Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0

Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…

Comment: Finding DEGs by using edgeR by prity6459 • 0

Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …

Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k

It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…

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A: Docker container with bioconductor and devtools

Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

Comment: DEXSeq DEXSeqDataSet count matrix duplication

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