Bioconductor Cnetplot

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cnetplot DESeq2

10 weeks ago Blandine • 0

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cnetplot R clusterProfiler

updated 2.1 years ago by Guido Hooiveld ★ 4.1k • written 2.1 years ago by YNKIM ▴ 10

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clusterProfiler enrichplot cnetplot GuangchuangYu

updated 2.6 years ago by Guangchuang Yu ★ 1.2k • written 2.9 years ago by adR ▴ 40

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clusterProfiler enrichKEGG cnetplot

3.4 years ago fatimaruizdelabastida ▴ 10

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clusterProfiler enrichplot cnetplot

updated 5.2 years ago by James W. MacDonald 68k • written 5.2 years ago by anders.tondell ▴ 30

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Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0

Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…

Answer: DESeq2 - am I extracting results incorrectly? by James W. MacDonald 68k

If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…

Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0

I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…

Answer: Origin of the labels for the SingleCellMultiModal dataset by ATpoint ★ 4.8k

If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…

Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by ATpoint ★ 4.8k

That plot looks extremely worrying. You have very unbalanced DE profiles and clearly two populations of peaks on the right. I would make su…

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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder

Comment: DESeq - help with pair wise comparisons

Answer: Is random access by row index possible for an indexed VCF file?

Answer: SingleR with multiple single cell references

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