Bioconductor RNA-Seq

Showing : RNA-Seq • reset

votes

replies

284

views

rna-seq edgeR

updated 4 days ago by Gordon Smyth 50k • written 17 days ago by Netanel • 0

votes

replies

7.8k

views

deseq2 edgeR rna-seq

updated 6 days ago by Elizabeth • 0 • written 8.8 years ago by gthm ▴ 30

votes

901

views

correlation pearsoncorrelation rna-seq differential gene expression

updated 4 months ago by ATpoint ★ 4.0k • written 6.0 years ago by saad_k6 • 0

votes

replies

300

views

RNA-Seq WGCNA Worms

5 months ago davca • 0

votes

replies

678

views

RNA-seq DESeq2

6 months ago ar14g12 • 0

votes

replies

3.5k

views

RNA-seq featureCounts ht-seq

written 3.8 years ago by ag1805x ▴ 80

votes

replies

1.5k

views

GeneExpression GenomicFeatures RNA-Seq TPM

updated 7 months ago by Gordon Smyth 50k • written 7 months ago by gingergeiger22 • 0

votes

replies

639

views

DEXSeq RNA-seq DESeq2

updated 7 months ago by Alejandro Reyes ★ 1.9k • written 7 months ago by Alice • 0

votes

replies

2.2k

views

Spike-in RNASeqR DESeq2 Normalization rna-seq

updated 7 months ago by manuel.fernandez • 0 • written 2.0 years ago by cicely.day • 0

votes

replies

849

views

BatchEffect lfcshrink RNA-seq DESeq2

8 months ago Eva ▴ 10

votes

replies

2.2k

views

isoformswitchanalyzeR rna-seq splice-variants

written 5.1 years ago by saddamhusain77 • 0

votes

replies

667

views

rna-seq salmon fishpond swish

updated 10 months ago by Michael Love 41k • written 10 months ago by samuelcjx • 0

votes

replies

1.2k

views

filtering RNA-Seq CPM edgeR filterByExpr

updated 11 months ago by Gordon Smyth 50k • written 11 months ago by mohammedtoufiq91 ▴ 10

votes

replies

1.2k

views

gage rna-seq pathwayanalysis

updated 11 months ago by Rob • 0 • written 3.5 years ago by microPhD • 0

votes

replies

837

views

RNA-Seq sequencer library_size sequency_depth multiplexing offtopic

updated 11 months ago by James W. MacDonald 65k • written 11 months ago by FedeXander • 0

votes

replies

700

views

RNA-Seq normalization PCR_efficiency bias intrasample_comparison

updated 11 months ago by James W. MacDonald 65k • written 11 months ago by FedeXander • 0

16 results • Page 1 of 1

Recent ...

Replies

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…

Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k

Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…

Votes

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Answer: Interpret plot from DiffBind

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0