Bioconductor Forum

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ensembl ensembldb plant arabidopsis thaliana annotationhub

updated 31 minutes ago by Johannes Rainer ★ 2.0k • written 5.5 years ago by Guido Hooiveld ★ 4.0k

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limma

2 days ago • updated 19 hours ago Anna • 0

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BatchQC BatchEffect rnaseqGene Normalization

updated 19 hours ago by James W. MacDonald 66k • written 1 day ago by Đình Vinh • 0

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128

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BatchQC BatchEffect RNASeq

updated 19 hours ago by James W. MacDonald 66k • written 1 day ago by ttt • 0

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affy

updated 18 hours ago by James W. MacDonald 66k • written 2 days ago by pickingastar • 0

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554

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DESeq2

3 days ago • updated 17 hours ago Ken C • 0

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146

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BatchQC batchinDeseq2. columnsincolData.

2 days ago • updated 21 hours ago Galina • 0

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apeglm

updated 16 hours ago by Michael Love 42k • written 1 day ago by euge.eugenio ▴ 20

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179

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DESeq2 PCAplot RNA-Seq DesignModel

updated 17 hours ago by Michael Love 42k • written 3 days ago by shaunpeterson • 0

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DESeq2

updated 14 hours ago by James W. MacDonald 66k • written 1 day ago by boczniak767 ▴ 720

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org.Rn.eg.db biomaRt

updated 42 minutes ago by blackwidowzzz • 0 • written 14 hours ago by landenshanie ▴ 40

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curl microRNA starBase webapi ENCORI

updated 23 hours ago by ATpoint ★ 4.1k • written 1 day ago by V_Vibes • 0

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735

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ENmix IlluminaHumanMethylationEPICmanifest

updated 14 hours ago by James W. MacDonald 66k • written 2.0 years ago by Daphna • 0

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AnnotationHub ExperimentHub

9 hours ago Tim Barry • 0

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StatisticalMethod Evolution QuantitativeTrailLocus Genetics JobPosting

19 hours ago pierre.devillemereuil • 0

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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k

You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…

Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0

I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …

Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k

If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …

Comment: Help with ENmix readidat by James W. MacDonald 66k

Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …

Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k

In that case, probably easiest to subset to the groups being compared.

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Comment: LRT, more than two conditions and pairwise comparisons

Answer: Control group between 2 batches have different expression in RNAseq data

Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?

Comment: DESeq2- Mysterious interaction suppresses DEGs

Answer: DESeq2- Mysterious interaction suppresses DEGs

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