Bioconductor Vranges

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1.9k

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variantannotation vcf readvcf vranges

updated 6.3 years ago by Michael Lawrence ★ 11k • written 6.3 years ago by david.mas • 0

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3.3k

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variantannotation granges DNAStringSetList findoverlaps Vranges

9.6 years ago summerela • 0

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2.3k

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SomaticSignatures mutationContext VRanges

updated 9.1 years ago by Julian Gehring ★ 1.3k • written 9.1 years ago by tesa.severson ▴ 10

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2.4k

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variantannotation vranges readvcf readvcfasvranges metadata

9.6 years ago summerela • 0

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1.6k

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granges vranges readvcfasvranges somaticsignatures

updated 8.5 years ago by Michael Lawrence ★ 11k • written 8.5 years ago by jpluta26 • 0

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2.0k

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somaticsignatures vranges

updated 8.3 years ago by Julian Gehring ★ 1.3k • written 8.3 years ago by arsala521 ▴ 10

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1.9k

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somaticsignatures somaticsignatures package readvcfasvranges vranges

7.2 years ago • updated 7.1 years ago guillaume.dachy • 0

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842

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somaticsignatures vranges readvcfasvranges

6.1 years ago guillaume.dachy • 0

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1.4k

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vranges vcf to vranges

7.8 years ago Bogdan ▴ 670

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1.3k

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variantannotation VRanges R Rle

updated 6.3 years ago by Valerie Obenchain ★ 6.8k • written 6.3 years ago by Jayendra Shinde • 0

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Comment: GSVA ssGSEA vs. Broad implementation of ssGSEA by Bob ▴ 10

Thanks for the prompt answer! I looked into the "original ssGSEA R-implementation" ([https://github.com/GSEA-MSigDB/ssGSEA-gpmodule][1]), u…

Comment: RNASeq Time Course Question by jihoon.kim.1495 ▴ 10

I see. You'd mean clustering using only the right 5 columns (in the above example), right?

Comment: RNASeq Time Course Question by Michael Love 42k

Yes. If you wanted to focus on differences, you could cluster on the subset of coefficients representing differences (interactions).

Comment: RNASeq Time Course Question by jihoon.kim.1495 ▴ 10

Thanks for the clarification. With regards to your last comment about the clustering by the coefficients/log2fold changes, I wanted to cl…

Answer: RNASeq Time Course Question by Michael Love 42k

> I am comparing Wildtype Day7 VS Condition Day 7, or is there a different comparison being made? yes. Remember, from the workflow, we sa…

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C: Vertical line at A=0, nothing else, on MA plot

Comment: RNASeq Time Course Question

Answer: RNASeq Time Course Question

Comment: limma plotMDS - logFC inverted?

DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)

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