Bioconductor Bugs

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bugs limma

8 months ago Zhenyu • 0

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1.2k

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arrayexpress affy bugs

updated 5.2 years ago by James W. MacDonald 63k • written 5.2 years ago by Ed Siefker ▴ 230

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1.5k

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GSVA bug gsva bugs

updated 5.7 years ago by Robert Castelo ★ 3.0k • written 5.7 years ago by JasonL_Weirather ▴ 10

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922

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DiffBind bugs

updated 6.0 years ago by Rory Stark ★ 4.8k • written 6.0 years ago by jeremydt • 0

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1.2k

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txdb.hsapiens.ucsc.hg19.knowngene seqlevels bugs

updated 6.5 years ago by Hervé Pagès 16k • written 6.5 years ago by wcstcyx ▴ 30

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965

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annotationhub bugs encode bed

6.5 years ago wcstcyx ▴ 30

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869

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bugs impute

6.7 years ago Shicheng Guo • 0

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1.4k

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software error bugs deseq2

updated 7.3 years ago by Michael Love 40k • written 7.3 years ago by john.hu • 0

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1.2k

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monocle bugs

7.5 years ago wanghao1993333 • 0

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1.3k

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ggbio bugs tracks autoplot

8.3 years ago cooketho • 0

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1.3k

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arrayqualitymetrics bugs error

updated 8.6 years ago by James W. MacDonald 63k • written 8.6 years ago by daugherty_a • 0

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1.8k

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Bugs deseq2

updated 8.7 years ago by Michael Love 40k • written 8.7 years ago by lmf.bill@gmail.com ▴ 10

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1.3k

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Bugs ggbio

8.7 years ago Anne Deslattes Mays ▴ 30

13 results • Page 1 of 1

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Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k

limma already adjusts for the baseline expression level of each subject. Trying to include baseline expression explicitly in the linear mod…

Comment: Remove duplicate genera in DEseq output? by ATpoint ★ 2.9k

This seems to be very specific rather than a general and technical DESeq2 question. See the last point of https://support.bioconductor.org/…

Comment: Use with_go along with other filters in getBM function by RuBBiT0 ▴ 10

Hi @mike-smith , you are correct. I was trying to select the ones that have some GO annotations by using the `with_go` filter. I was confus…

Answer: Can VST-transformed community composition data be expressed as relative abundanc by Michael Love 40k

The point of the VST is to make the data systematically homoskedastic (that is, not systematic trend of variance over mean, but not e.g. fo…

Comment: How to update a package at Bioconductor by ma79 • 0

thanks, just informed the original maintainer to send an email.

Votes

A: Using R package 'limma' on pre-normalized counts and the effect of non-equivalen

Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model

A: What can I do if I only have TPM but not raw counts data?

What can I do if I only have TPM but not raw counts data?

Differential expression of FPKM from RNA-seq data using limma and voom()

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Teacher to deeenes ▴ 30