Bioconductor S4

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genomicranges grangeslist granges s4

updated 2.1 years ago by Hervé Pagès 16k • written 7.9 years ago by richierocks ▴ 40

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updated 9.0 years ago by Michael Lawrence ★ 11k • written 9.0 years ago by Koen Van den Berge ▴ 180

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lumi S4

9.1 years ago Chi Hong • 0

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rnbeads error as.vector(data) s4vectors s4

8.6 years ago schasse • 0

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mclust s4vectors S4 as.matrix .FCS

7.8 years ago anara92 • 0

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s4 coercion iranges integerlist

7.7 years ago jian_liangli • 0

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iranges integerlist s4

7.7 years ago Jurat Shahidin ▴ 80

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devtools S4 methods cache

5.4 years ago Michael Steinbaugh ▴ 90

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s4 methods SummarizedExperiment

updated 5.2 years ago by Aaron Lun ★ 28k • written 5.2 years ago by brendan.innes ▴ 20

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s4 dataframe left_join merge

updated 5.0 years ago by Hervé Pagès 16k • written 5.0 years ago by Michael Steinbaugh ▴ 90

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998

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DBI S4 Biobase

updated 20 months ago by Hervé Pagès 16k • written 20 months ago by sandmann.t ▴ 70

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989

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S4 packages

updated 5.7 years ago by Michael Lawrence ★ 11k • written 5.7 years ago by lukaszbednarz ▴ 10

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s4 generic

updated 5.2 years ago by Marcel Ramos 690 • written 5.2 years ago by Michael Steinbaugh ▴ 90

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830

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S4 Rcpp InteractionSet IRanges Rle

updated 3.9 years ago by Aaron Lun ★ 28k • written 3.9 years ago by lklei001 • 0

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calcium imaging imaging s4

updated 4.1 years ago by shepherl 3.8k • written 4.1 years ago by muad.abdelhay ▴ 10

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S4 deseq2

updated 5.2 years ago by swbarnes2 ★ 1.3k • written 5.2 years ago by shintzen • 0

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650

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class S4

updated 4.2 years ago by Hervé Pagès 16k • written 4.2 years ago by Teun van den Brand • 0

17 results • Page 1 of 1

Recent ...

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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…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

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

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

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?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0