Bioconductor Smallrna

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smallrna counts

7.6 years ago ribioinfo ▴ 100

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TMM deseq2 smallrna rnaseq

updated 5.4 years ago by António Miguel de Jesus Domingues ▴ 510 • written 5.4 years ago by Konstantinos Yeles ▴ 80

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Transcription Sequencing miRNA SmallRNA Annotation Normalization GO Cancer Organism edgeR

updated 11.6 years ago by Steve Lianoglou ★ 13k • written 11.6 years ago by Weng Khong LIM ▴ 10

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Sequencing SmallRNA Microarray limma Sequencing SmallRNA Microarray limma

updated 9.7 years ago by James W. MacDonald 65k • written 9.7 years ago by Jakub Stanislaw Nowak ▴ 70

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Sequencing miRNA SmallRNA DESeq Sequencing miRNA SmallRNA DESeq

updated 13.4 years ago by Wolfgang Huber ★ 13k • written 13.4 years ago by Wu, Xiwei ▴ 350

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Sequencing SmallRNA edgeR Sequencing SmallRNA edgeR

updated 11.6 years ago by Mark Robinson ▴ 880 • written 11.6 years ago by Danie ▴ 40

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counts SmallRNA Normalization

updated 2.4 years ago by hauken_heyken ▴ 80 • written 2.5 years ago by k___ ▴ 30

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694

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SmallRNA DESeq2

21 months ago jucosie • 0

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679

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DESeq2 SmallRNA

updated 9 weeks ago by Michael Love 41k • written 9 weeks ago by r.r.bioinf • 0

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matrix DESeq2 SmallRNA dimensions small

2.6 years ago andreia ▴ 10

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mirna riboseq smallrna differential gene expression Job

6.1 years ago Andy Lynch ▴ 120

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cancer sequencing rnaseq methylation smallrna Job

5.9 years ago Andy Lynch ▴ 120

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deseq2 normalization smallrna ribosomal rna

7.6 years ago mosharrofgeb ▴ 10

13 results • Page 1 of 1

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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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