Bioconductor Rstudio

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DESeq2 RSTUDIO PCAtools

updated 4 hours ago by ATpoint ★ 4.0k • written 20 hours ago by Aaliya • 0

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224

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RStudio ggkegg

updated 4 months ago by James W. MacDonald 65k • written 4 months ago by Ramirj49 • 0

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477

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Rstudio cDNA ensembldb NCBI

4 months ago R_Page • 0

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337

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Rstudio plotPCA DESeq2

5 months ago • updated 4 months ago yee • 0

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444

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AccNo OrgDb convert Organismname RStudio

updated 5 months ago by James W. MacDonald 65k • written 5 months ago by j_denton • 0

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752

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RStudio convert ensembldb NCBI

5 months ago j_denton • 0

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1.5k

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error RStudio ggplot2 DESeq2

updated 5 months ago by James W. MacDonald 65k • written 5 months ago by BioES • 0

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378

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Rstudio scRNAseq DESeq2

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

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982

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scRNAseq RStudio DESeq2

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

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5.7k

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Ensembl Rstudio ensembldb AnnotationHub ensdb

updated 6 weeks ago by shepherl 3.8k • written 2.2 years ago by jon.klonowski ▴ 40

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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k

an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.

Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k

Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…

Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20

Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…

Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k

The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…

Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k

Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…

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C: SGSeq: moving toward diffex from SGSeq analysis

DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds

Subset DEXSeqDataSet In DEXSeq

How to get all possible comparisons in DiffBind

Comment: get BM error

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Scholar to ATpoint ★ 4.0k