Bioconductor Seqgsea

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limma deseq2 seqgsea sva deseq

5.6 years ago kentfung ▴ 20

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seqgsea

updated 8.5 years ago by Martin Morgan 25k • written 8.5 years ago by jial2 • 0

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1.3k

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goseq SeqGSEA goseq SeqGSEA

updated 9.2 years ago by Xi Wang • 0 • written 11.7 years ago by Julie Leonard ▴ 110

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Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI

updated 10.9 years ago by Steve Lianoglou ★ 13k • written 10.9 years ago by Leif Väremo ▴ 70

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Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA

updated 10.9 years ago by Julian Gehring ★ 1.3k • written 10.9 years ago by enricoferrero ▴ 680

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Comment: plyranges: find exact GRanges match keeping metadata columns by alexis.weinreb • 0

Thank you, this does clarify the available options.

Answer: displaying the differential expression with deseq2 over 4X2 samples with the in by James W. MacDonald 67k

If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…

Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by jodan • 0

Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…

Answer: Unused arguments error without used arguments in GSVA? by jodan • 0

It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…

Answer: Using genomicRanges / plyranges to calculate score of peaks within intervals by Michael Love 43k

This should be possible with plyranges using `join_overlap` and `group_by` on the metadata from the tile. E.g. create `tile.id` as a variab…

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