Bioconductor Rna seq

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4.0k

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deseq2 mahattan plot RNA Seq

updated 5.0 years ago by bernatgel ▴ 150 • written 6.0 years ago by adeler001 • 0

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4.8k

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batch effect limma rna seq DE

updated 5.5 years ago by Steve Lianoglou ★ 13k • written 5.5 years ago by svlachavas ▴ 840

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1.4k

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RNA seq cpm

updated 5.6 years ago by Kevin Blighe ★ 4.0k • written 5.6 years ago by isabel.pieterse • 0

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1.5k

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sgseq alternative splicing rna seq

updated 15 months ago by Sara • 0 • written 5.9 years ago by 116100016 • 0

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1.3k

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edger RNA Seq

updated 5.9 years ago by James W. MacDonald 68k • written 5.9 years ago by abf ▴ 30

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806

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rna seq

5.9 years ago adeler001 • 0

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1.3k

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rna seq SGSeq Alternative splicing

updated 6.0 years ago by Leonard Goldstein ▴ 260 • written 6.0 years ago by 116100016 • 0

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813

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deseq2 likelihood ratio rna seq wald test

updated 6.1 years ago by Michael Love 43k • written 6.1 years ago by adeler001 • 0

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1.4k

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volcano plot rna seq

updated 6.2 years ago by Michael Love 43k • written 6.2 years ago by adeler001 • 0

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1.8k

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limma voom RNA Seq Time-course experiments

updated 6.4 years ago by Aaron Lun ★ 29k • written 6.4 years ago by mahes.muniandy • 0

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1.7k

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RNA seq wgcna

updated 6.4 years ago by Peter Langfelder ★ 3.0k • written 6.4 years ago by agustin.gonvi ▴ 20

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2.7k

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rna seq trimmomatic trimming adapter trimming paired analysis

6.5 years ago Mozart ▴ 30

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2.2k

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heatmap.2 hierarchical clustering microarray RNA seq DEG

7.7 years ago lawarde.ankita1 ▴ 30

13 results • Page 1 of 1

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Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

Comment: deseq2 filter the low counts by empty_mt • 0

Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…

Comment: DESeq2 interactions by Michael Love 43k

GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …

Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k

We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you

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Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

Answer: DESeq2 for candidate gene analysis

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