Bioconductor HTSeqCounts

Showing : HTSeqCounts • reset

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1.5k

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deseq2 deseq edgeR rnaseq htseqcounts

6.8 years ago Deepali • 0

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2.1k

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edger htseqcounts

updated 6.8 years ago by Gordon Smyth 51k • written 6.8 years ago by Bioinformatics ▴ 30

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2.3k

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R summarizeoverlaps htseqcounts

updated 7.1 years ago by thokall ▴ 160 • written 7.1 years ago by Walter F. Baumann ▴ 10

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4.7k

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htseqcounts edger

updated 2.1 years ago by Randy • 0 • written 7.2 years ago by mictadlo ▴ 10

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3.5k

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edger htseqcounts

updated 7.2 years ago by Gordon Smyth 51k • written 7.2 years ago by mictadlo ▴ 10

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1.3k

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htseqcounts star rnaseq

7.2 years ago Ahdee ▴ 50

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2.6k

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featurecounts SAM htseqcounts

updated 16 months ago by Yang Liao ▴ 450 • written 7.5 years ago by courtney.stairs • 0

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3.8k

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chipseq deseq2 htseqcounts

updated 21 months ago by mhashan.j ▴ 10 • written 7.8 years ago by JunLVI ▴ 40

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1.2k

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edger htseqcounts rnaseq

updated 7.9 years ago by Aaron Lun ★ 28k • written 7.9 years ago by romsdahl • 0

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1.2k

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dexseq_count dexseq htseqcounts

8.2 years ago as1023 • 0

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1.9k

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deseq2 pca tximportdata htseqcounts

updated 8.4 years ago by Michael Love 42k • written 8.4 years ago by jarod_v6@libero.it ▴ 40

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deseq2 goseq htseqcounts rnaseq plant

updated 8.5 years ago by Gordon Smyth 51k • written 8.5 years ago by Ben Mansfeld • 0

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HTSeq HTSeqCounts Could not find function DEXSeq

updated 8.6 years ago by Martin Morgan 25k • written 8.6 years ago by sakura.nussbaum ▴ 10

13 results • Page 1 of 1

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Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0

The updated version worked well on my data. Thank you!

Votes

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

A: Error in DESeqDataSet : some values in assay are not integers

Awards • All

Scholar to Haibo Liu ▴ 20