Bioconductor ClusterProfiler

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164

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Pathways clusterProfiler gseKEGG KEGG

12 days ago • updated 11 days ago julia_mcdonough • 0

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136

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clusterProfiler OrgDb biomaRt Zea_mays

updated 5 days ago by James W. MacDonald 65k • written 5 days ago by sansan • 0

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109

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clusterProfiler GeneSetEnrichment

8 days ago Ana • 0

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210

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clusterProfiler GenomicDistributionsData KEGG

updated 8 hours ago by Guido Hooiveld ★ 3.9k • written 3 days ago by fernanda.backsouza ▴ 10

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809

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clusterProfiler RNASeq

updated 8 hours ago by Guangchuang Yu ★ 1.2k • written 13 months ago by ruiqi.li ▴ 10

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KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware

updated 1 day ago by James W. MacDonald 65k • written 1 day ago by fernanda.backsouza ▴ 10

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129

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DOSE enrichplot clusterProfiler

updated 10 days ago by Guido Hooiveld ★ 3.9k • written 13 days ago by Lucie • 0

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159

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clusterProfiler ggpubr

updated 16 days ago by James W. MacDonald 65k • written 16 days ago by BCS12 • 0

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129

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clusterProfiler gseKEGG

19 days ago andromeda • 0

9 results • Page 1 of 1

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by marka • 0

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Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Comment: get BM error by Fara • 0

Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…

Votes

Answer: get BM error

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

Comment: Different Shrunk Log2FC according with reference

Reproducibility issue with scran together with lapply and BiocParallel

C: SGSeq: moving toward diffex from SGSeq analysis

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