Bioconductor RNA Seq

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2.7k

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deseq2 mahattan plot RNA Seq

updated 3.7 years ago by bernatgel ▴ 150 • written 4.7 years ago by adeler001 • 0

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3.3k

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batch effect limma rna seq DE

updated 4.2 years ago by Steve Lianoglou ★ 13k • written 4.2 years ago by svlachavas ▴ 830

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679

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RNA seq cpm

updated 4.2 years ago by Kevin Blighe ★ 3.9k • written 4.2 years ago by isabel.pieterse • 0

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920

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sgseq alternative splicing rna seq

updated 4.6 years ago by Leonard Goldstein ▴ 220 • written 4.6 years ago by 116100016 • 0

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919

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edger RNA Seq

updated 4.6 years ago by James W. MacDonald 66k • written 4.6 years ago by abf ▴ 30

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509

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rna seq

4.6 years ago adeler001 • 0

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811

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rna seq SGSeq Alternative splicing

updated 4.7 years ago by Leonard Goldstein ▴ 220 • written 4.7 years ago by 116100016 • 0

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565

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deseq2 likelihood ratio rna seq wald test

updated 4.7 years ago by Michael Love 42k • written 4.8 years ago by adeler001 • 0

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974

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volcano plot rna seq

updated 4.8 years ago by Michael Love 42k • written 4.8 years ago by adeler001 • 0

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1.3k

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limma voom RNA Seq Time-course experiments

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by mahes.muniandy • 0

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1.0k

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RNA seq wgcna

updated 5.0 years ago by Peter Langfelder ★ 3.0k • written 5.0 years ago by agustin.gonvi ▴ 20

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1.9k

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rna seq trimmomatic trimming adapter trimming paired analysis

5.1 years ago Mozart ▴ 30

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1.6k

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heatmap.2 hierarchical clustering microarray RNA seq DEG

6.3 years ago lawarde.ankita1 ▴ 30

13 results • Page 1 of 1

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Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100

Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz

Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k

The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …

Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k

You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.

Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0

In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…

Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k

For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…

Votes

Answer: How to do DESeq2 on Kallisto Data

Comment: Most enriched pathway is not expressed when modifying universe parameter

Time-course, comparison of two groups

Answer: Behaviour of featureCounts when quantifying multi-mapping reads

Answer: GESA with certain gene list returns no result with human genom, but many result

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