Bioconductor Rle

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RLE normalization deseq2

updated 23 months ago by ATpoint ★ 4.7k • written 23 months ago by SH ▴ 10

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S4 Rcpp InteractionSet IRanges Rle

updated 4.7 years ago by Aaron Lun ★ 28k • written 4.7 years ago by lklei001 • 0

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deseq2 RLE

updated 5.1 years ago by Michael Love 43k • written 5.1 years ago by f_pardow • 0

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variantannotation VRanges R Rle

updated 6.7 years ago by Valerie Obenchain ★ 6.8k • written 6.7 years ago by Jayendra Shinde • 0

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iranges s4vectors rle rlelist

6.7 years ago endrebak85 ▴ 40

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rle deseq2 normalization

updated 6.8 years ago by Michael Love 43k • written 6.8 years ago by Aurora ▴ 20

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Rle Big data coverageByTranscript

6.9 years ago hauken_heyken ▴ 80

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delayedarray rlelist rle

updated 7.3 years ago by Peter Hickey ▴ 750 • written 7.3 years ago by davide risso ▴ 980

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DataFrame Rle generic expression table

updated 20 months ago by Hervé Pagès 16k • written 7.8 years ago by Charles Plessy ▴ 180

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Rle granges iranges

8.4 years ago my4 ▴ 10

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granges Rle coverage View mean

updated 8.7 years ago by Michael Lawrence ★ 11k • written 8.7 years ago by Christian Ruckert ▴ 170

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biostrings coverage rle iranges

8.8 years ago likeeatingpizza ▴ 10

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rle normalization table

updated 9.4 years ago by Steve Lianoglou ★ 13k • written 9.4 years ago by aiko • 0

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RLE GenomicFeatures rnaseq

updated 9.9 years ago by Hervé Pagès 16k • written 9.9 years ago by gen ▴ 30

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RLE iranges granges coverage

updated 9.9 years ago by Martin Morgan 25k • written 9.9 years ago by gen ▴ 30

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rle list irange grangeslist

updated 9.9 years ago by Chris Seidel ▴ 80 • written 9.9 years ago by gen ▴ 30

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rle Views

10.0 years ago Sean Davis 21k

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views iranges rle

10.1 years ago Janet Young ▴ 740

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affyPLM RLE NUSE

updated 10.1 years ago by Sean Davis 21k • written 10.1 years ago by beverly893 ▴ 10

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Rle boxplot

10.1 years ago Johannes Rainer ★ 2.1k

20 results • Page 1 of 1

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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k

If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…

Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0

why aren't there any answers?

Comment: Too many significant genes when integrating gtex and tcga by Jane • 0

I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…

Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180

Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…

Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k

No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…

Votes

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

Answer: Group-specific condition effects with individuals nested: matrix is not full ra

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