Bioconductor Read counting

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1.1k

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read counting CNV rsamtools

updated 6.7 years ago by James W. MacDonald 67k • written 6.7 years ago by Bogdan ▴ 670

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1.3k

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featurecounts read counting

updated 6.7 years ago by Gordon Smyth 51k • written 6.7 years ago by marc.gabriel.01 • 0

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2.3k

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diffbind read counting warning message chromatin atac-seq

updated 7.0 years ago by Gord Brown ▴ 670 • written 7.0 years ago by tgjohnst • 0

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2.3k

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Gviz sashimi sashimi plots read counting bam

updated 7.7 years ago by Robert Ivanek ▴ 750 • written 7.7 years ago by bernt.popp • 0

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3.1k

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summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting

8.4 years ago ErickF ▴ 40

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4.2k

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genomicalignments read counting

9.2 years ago kgorczak ▴ 10

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Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0

Thank you!

Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0

Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…

Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0

> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…

Comment: EuroBioC2024 abstract submission is open! by Esperan • 0

Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…

Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k

I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…

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Answer: Combining RNAseq and microarray data using edgeR/limma-voom

Answer: How do I merge a list of GRanges?

A: p.adjust BH generates duplicate values

Answer: Adjusted p-values become NA when sub-setting samples

Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice

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