Bioconductor Bugs

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1.8k

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bugs limma

2.1 years ago Zhenyu • 0

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2.2k

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Bugs deseq2

updated 10.0 years ago by Michael Love 42k • written 10.0 years ago by lmf.bill@gmail.com ▴ 10

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2.7k

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GSVA bug gsva bugs

updated 7.0 years ago by Robert Castelo ★ 3.4k • written 7.0 years ago by JasonL_Weirather ▴ 10

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1.8k

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software error bugs deseq2

updated 8.7 years ago by Michael Love 42k • written 8.7 years ago by john.hu • 0

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1.6k

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arrayqualitymetrics bugs error

updated 9.9 years ago by James W. MacDonald 67k • written 9.9 years ago by daugherty_a • 0

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1.4k

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annotationhub bugs encode bed

7.8 years ago wcstcyx ▴ 30

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1.6k

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txdb.hsapiens.ucsc.hg19.knowngene seqlevels bugs

updated 7.8 years ago by Hervé Pagès 16k • written 7.8 years ago by wcstcyx ▴ 30

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1.2k

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DiffBind bugs

updated 7.4 years ago by Rory Stark ★ 5.2k • written 7.4 years ago by jeremydt • 0

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1.7k

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arrayexpress affy bugs

updated 6.6 years ago by James W. MacDonald 67k • written 6.6 years ago by Ed Siefker ▴ 230

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1.7k

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ggbio bugs tracks autoplot

9.7 years ago cooketho • 0

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1.2k

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bugs impute

8.1 years ago Shicheng Guo • 0

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1.6k

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monocle bugs

8.9 years ago wanghao1993333 • 0

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1.5k

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Bugs ggbio

10.1 years ago Anne Deslattes Mays ▴ 30

13 results • Page 1 of 1

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Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet by Gordon Smyth 51k

Thanks very much for the reproducible example. The bug has been fixed now in edgeR 4.3.17 on the Bioconductor developmental repository.

Answer: Highly DE genes but small count difference within conditions by h1vu81gcd7 • 0

It sounds like you're diving deep into DE analysis, comparing condition1 with the control using a solid design. However, the elevated padj …

Comment: dmpFinder for other objects by neyousha • 0

Hi James, Thank you a lot for responding. Hmm... so do you think if have matrix average_beta below: ![average_beta_matrix][1] [1]:…

Comment: DEseq2 time-series design by Michael Love 42k

Would you mind making a new post -- it's just easier for threaded content. And feel free to post any particular code or images you need.

Comment: Rsubread alignment crashes at 35%, valgrind indicates invalid writes by Yang Liao ▴ 440

Thanks for taking the time to report the bug! The provided `Valgrind` report is very helpful and suggests the issue lies within the banded …

Votes

Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet

Answer: dmpFinder for other objects

GSVA ssGSEA vs. Broad implementation of ssGSEA

Answer: How to control batch effect if Group and batch are same?

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