Bioconductor RNA Seq

Showing : RNA Seq • reset

votes

replies

3.3k

views

deseq2 mahattan plot RNA Seq

updated 4.2 years ago by bernatgel ▴ 150 • written 5.2 years ago by adeler001 • 0

votes

replies

3.9k

views

batch effect limma rna seq DE

updated 4.7 years ago by Steve Lianoglou ★ 13k • written 4.7 years ago by svlachavas ▴ 840

votes

replies

949

views

RNA seq cpm

updated 4.7 years ago by Kevin Blighe ★ 4.0k • written 4.7 years ago by isabel.pieterse • 0

votes

replies

1.2k

views

sgseq alternative splicing rna seq

updated 5 months ago by Sara • 0 • written 5.1 years ago by 116100016 • 0

vote

replies

1.1k

views

edger RNA Seq

updated 5.1 years ago by James W. MacDonald 67k • written 5.1 years ago by abf ▴ 30

votes

replies

661

views

rna seq

5.1 years ago adeler001 • 0

votes

replies

1.0k

views

rna seq SGSeq Alternative splicing

updated 5.2 years ago by Leonard Goldstein ▴ 260 • written 5.2 years ago by 116100016 • 0

votes

677

views

deseq2 likelihood ratio rna seq wald test

updated 5.3 years ago by Michael Love 43k • written 5.3 years ago by adeler001 • 0

votes

replies

1.2k

views

volcano plot rna seq

updated 5.3 years ago by Michael Love 43k • written 5.3 years ago by adeler001 • 0

vote

replies

1.5k

views

limma voom RNA Seq Time-course experiments

updated 5.5 years ago by Aaron Lun ★ 28k • written 5.5 years ago by mahes.muniandy • 0

votes

replies

1.3k

views

RNA seq wgcna

updated 5.6 years ago by Peter Langfelder ★ 3.0k • written 5.6 years ago by agustin.gonvi ▴ 20

vote

replies

2.3k

views

rna seq trimmomatic trimming adapter trimming paired analysis

5.7 years ago Mozart ▴ 30

votes

replies

1.9k

views

heatmap.2 hierarchical clustering microarray RNA seq DEG

6.9 years ago lawarde.ankita1 ▴ 30

13 results • Page 1 of 1

Recent ...

Replies

Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…

Votes

A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

Awards • All