Bioconductor RNA-seq

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deseq2 edgeR rna-seq

updated 13 days ago by Elizabeth • 0 • written 8.8 years ago by gthm ▴ 30

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filtering RNA-Seq CPM edgeR filterByExpr

updated 11 months ago by Gordon Smyth 50k • written 11 months ago by mohammedtoufiq91 ▴ 10

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312

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rna-seq edgeR

updated 10 days ago by Gordon Smyth 50k • written 23 days ago by Netanel • 0

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862

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BatchEffect lfcshrink RNA-seq DESeq2

8 months ago Eva ▴ 10

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GeneExpression GenomicFeatures RNA-Seq TPM

updated 7 months ago by Gordon Smyth 50k • written 7 months ago by gingergeiger22 • 0

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696

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RNA-seq DESeq2

7 months ago • updated 6 months ago ar14g12 • 0

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isoformswitchanalyzeR rna-seq splice-variants

written 5.1 years ago by saddamhusain77 • 0

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677

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rna-seq salmon fishpond swish

updated 10 months ago by Michael Love 41k • written 10 months ago by samuelcjx • 0

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709

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RNA-Seq normalization PCR_efficiency bias intrasample_comparison

updated 11 months ago by James W. MacDonald 65k • written 11 months ago by FedeXander • 0

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649

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DEXSeq RNA-seq DESeq2

updated 8 months ago by Alejandro Reyes ★ 1.9k • written 8 months ago by Alice • 0

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847

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RNA-Seq sequencer library_size sequency_depth multiplexing offtopic

updated 11 months ago by James W. MacDonald 65k • written 11 months ago by FedeXander • 0

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906

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correlation pearsoncorrelation rna-seq differential gene expression

updated 4 months ago by ATpoint ★ 4.1k • written 6.0 years ago by saad_k6 • 0

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309

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RNA-Seq WGCNA Worms

5 months ago davca • 0

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2.3k

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Spike-in RNASeqR DESeq2 Normalization rna-seq

updated 8 months ago by manuel.fernandez • 0 • written 2.1 years ago by cicely.day • 0

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gage rna-seq pathwayanalysis

updated 11 months ago by Rob • 0 • written 3.5 years ago by microPhD • 0

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RNA-seq featureCounts ht-seq

written 3.8 years ago by ag1805x ▴ 80

16 results • Page 1 of 1

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Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k

I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …

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…

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Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

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

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Scholar to Rory Stark ★ 5.2k

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