Bioconductor HELP

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bachelorthesis help HELP

updated 8 months ago by DrFizz • 0 • written 8 months ago by melander • 0

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DESeq2 HELP

14 months ago Michael • 0

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1.2k

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DESeq2 volcanoplot deseq HELP contrast

updated 14 months ago by Basti ▴ 780 • written 14 months ago by Michael • 0

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710

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ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene

18 months ago michela ▴ 20

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HELP HelloRanges

updated 18 months ago by James W. MacDonald 65k • written 18 months ago by michela ▴ 20

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HELP ChIC.data PeakDetection ChipOnChipData

18 months ago michela ▴ 20

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565

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HELP Data

updated 20 months ago by Guido Hooiveld ★ 3.9k • written 20 months ago by mcclurejenniferc • 0

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STRINGdb HELP

updated 14 months ago by Rodrigo ▴ 10 • written 2.2 years ago by Jessica ▴ 10

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HELP ChIPpeakAnno

2.5 years ago lexi.kellington • 0

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help DESeq2 DESeqDataSetFromMatrix rownames

updated 22 months ago by Sanatan • 0 • written 3.0 years ago by dorina.jamniczky • 0

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RNASeqData RNASeq GEO RNASeqR HELP

3.1 years ago hgalmoore • 0

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help software error

updated 5.3 years ago by Martin Morgan 25k • written 5.3 years ago by mafusa20 • 0

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limma time series help

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by rm1238 • 0

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clusterprofiler input files error help

updated 7.1 years ago by Guangchuang Yu ★ 1.2k • written 7.1 years ago by Mataivic • 0

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2.5k

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edger differential gene expression without replicate nested design help

updated 7.8 years ago by Aaron Lun ★ 28k • written 7.8 years ago by knipehf • 0

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R deseq2 differential gene expression help

7.9 years ago • updated 7.8 years ago fischer87 • 0

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1.3k

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limma help

updated 8.4 years ago by svlachavas ▴ 830 • written 8.4 years ago by libya.tahani • 0

17 results • Page 1 of 1

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre

Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k

Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…

Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0

Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

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

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0