Bioconductor Bugs

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bugs limma

2.4 years ago Zhenyu • 0

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arrayexpress affy bugs

updated 6.9 years ago by James W. MacDonald 67k • written 6.9 years ago by Ed Siefker ▴ 230

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2.9k

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GSVA bug gsva bugs

updated 7.3 years ago by Robert Castelo ★ 3.4k • written 7.3 years ago by JasonL_Weirather ▴ 10

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1.3k

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DiffBind bugs

updated 7.7 years ago by Rory Stark ★ 5.2k • written 7.7 years ago by jeremydt • 0

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1.7k

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txdb.hsapiens.ucsc.hg19.knowngene seqlevels bugs

updated 8.1 years ago by Hervé Pagès 16k • written 8.1 years ago by wcstcyx ▴ 30

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1.5k

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annotationhub bugs encode bed

8.2 years ago • updated 8.1 years ago wcstcyx ▴ 30

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1.2k

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bugs impute

8.4 years ago Shicheng Guo • 0

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1.9k

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software error bugs deseq2

updated 9.0 years ago by Michael Love 43k • written 9.0 years ago by john.hu • 0

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1.6k

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monocle bugs

9.2 years ago wanghao1993333 • 0

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1.8k

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ggbio bugs tracks autoplot

10.0 years ago cooketho • 0

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1.7k

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arrayqualitymetrics bugs error

updated 10.2 years ago by James W. MacDonald 67k • written 10.2 years ago by daugherty_a • 0

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2.2k

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Bugs deseq2

updated 10.4 years ago by Michael Love 43k • written 10.4 years ago by lmf.bill@gmail.com ▴ 10

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1.6k

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Bugs ggbio

10.4 years ago Anne Deslattes Mays ▴ 30

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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k

FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…

Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10

I see. Thank you ATpoint!

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0

Thanks James!

Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k

I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…

Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10

Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…

Votes

A: PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?

PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?

Bioconductor Course, Kenya 2025: Applications Open!

Comment: can't install tscR

Answer: Csaw normalization strategies - general inquiry

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