Bioconductor Genes

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DESeq2 genes Differential expressed

11 months ago Syed Zaheer ▴ 10

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1.1k

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topGO significant enrichment genes IDs

5.3 years ago David ROUX ▴ 20

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1.3k

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edger differential expression genes fold change

updated 4.8 years ago by Aaron Lun ★ 28k • written 4.9 years ago by ilovesuperheroes1993 • 0

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697

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deseq2 genes expression

updated 5.1 years ago by Michael Love 41k • written 5.1 years ago by UserAnonyme • 0

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1.2k

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datasets genes gene expression

updated 8.7 years ago by Steve Lianoglou ★ 13k • written 8.7 years ago by vavecilla • 0

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2.6k

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deseq2 wald lrt genes significance

updated 7.9 years ago by Michael Love 41k • written 7.9 years ago by aziza ▴ 20

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701

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deseq2 genes

updated 7.7 years ago by Michael Love 41k • written 7.7 years ago by silviajserrano • 0

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912

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deseq2 variance genes

updated 6.4 years ago by Michael Love 41k • written 6.4 years ago by hs.lansdell ▴ 20

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2.4k

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heatmap rownames genes

8.6 years ago johnlee.johnson • 0

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607

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R microRNA genes binding Site

4.8 years ago pengu447 • 0

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874

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GeneSetEnrichment genes genetogo

updated 22 months ago by Basti ▴ 780 • written 22 months ago by Noy • 0

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1.1k

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cnv genes genomic ranges splitByOverlap

updated 7.1 years ago by Martin Morgan 25k • written 7.1 years ago by julrodr80 ▴ 30

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Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…

Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0

Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

Comment: DEseq2 coefficient by JKim • 0

Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…

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SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

Make custom Txdb class objects from Txdb

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