Bioconductor Timecoursedata

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1.4k

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limma proteomics TMTlabeling timecoursedata

updated 3.4 years ago by SamGG ▴ 350 • written 3.5 years ago by maleknias • 0

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1.3k

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timecoursedata limma

7 months ago • updated 4 months ago triZZla • 0

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945

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QTL fourier TimeSeriesExperiment timecoursedata

3.0 years ago Daphne • 0

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864

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time-series DESeq2 RNASeq timecoursedata TimeCourse

updated 8 months ago by ATpoint ★ 4.0k • written 8 months ago by Debebe • 0

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624

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DESeq2 timecoursedata replicates

updated 13 months ago by Michael Love 41k • written 13 months ago by fepesanz8 • 0

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602

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DESeq2 time-series timecoursedata timecourse multifactorial

updated 16 months ago by Michael Love 41k • written 17 months ago by arshad1292 • 0

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481

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timecoursedata RNASeqData TimeCourse DESeq2

updated 9 months ago by Michael Love 41k • written 9 months ago by georgii.vdovin • 0

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471

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timecoursedata edgeR

updated 13 months ago by Gordon Smyth 50k • written 13 months ago by boczniak767 ▴ 720

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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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