Showing : DESEq2 • reset
0
votes
2
replies
1.2k
views
DESeq2 Complex Model
deseq2 rnaseq
updated 5.8 years ago by ★ 13k • written 5.8 years ago by ▴ 10
2
votes
3
replies
4.5k
views
Change axis scale for plotting PCA in DESeq2
deseq2
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
2
votes
13
replies
2.1k
views
DESeq2 normalization resulting in very different Total read counts for samples
deseq2 normalization
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
2
replies
1.2k
views
DESeq2 design formula
deseq2 design formula
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
0
votes
10
replies
4.1k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
0
votes
1
reply
917
views
LFC shrinkage Normal_vs_apeglm
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
1
vote
4
replies
1.0k
views
Design matrix design for the differentially expression analysis
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
0
votes
2
replies
2.3k
views
How should I normalize my RNAseq data from Polysome profiling
deseq2 bioconductor RNAseq normalization Polysome_profiling
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
1.6k
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
485
views
Add basemean of "condition A" and "condition B" to the final table
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
2.3k
views
DESeq2 plotCounts() function?
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
0
votes
2
replies
490
views
Raw RNAseq data upload in DEseq2
deseq2
5.8 years ago golam.mohiuddin • 0
6
votes
5
replies
4.1k
views
VST for scRNA-seq
deseq2 rnaseq normalization
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 50
1
vote
6
replies
2.0k
views
DESeq2 Normalisation out of excel data?
deseq2
5.8 years ago mueslirapper • 0
6
votes
13
replies
1.6k
views
DeSeq2 - adjusted p-value changes substantially after including non-coding RNA [SOLVED]
deseq2
5.8 years ago David Eccles (gringer) ▴ 30
0
votes
2
replies
1.3k
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
3
votes
5
replies
2.3k
views
How to extract DESeq2 results for an interaction design
deseq2 interaction
updated 5.8 years ago by ▴ 60 • written 5.8 years ago by • 0
11
votes
2
replies
6.5k
views
Filtering low variance genes for WGCNA
deseq2 WGCNA
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 40
0
votes
4
replies
1.2k
views
Normalizing for both gene size and library composition
RNA-seq normalization deseq2
updated 5.8 years ago by 43k • written 5.9 years ago by ▴ 40
0
votes
7
replies
1.9k
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
5.8 years ago MANYA_BIOINFO • 0
1
vote
4
replies
1.3k
views
Help with Deseq2 design
deseq2 design multifactor
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
3
replies
1.6k
views
Biplot environmental variables on top of PCA
deseq2 biplot plotpca
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 30
1
vote
4
replies
2.1k
views
install DESeq2 failed
deseq2
5.9 years ago petitechiarina • 0
0
votes
2
replies
647
views
Data normalization when genes have global alter
deseq2
written 5.9 years ago by • 0
4
votes
5
replies
978
views
apparent DESeq2::DESeq() performance decline since v1.22.2
DESeq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
vote
2
replies
1.3k
views
Time series experiment analysis in DEseq2 without T=0 and three independent experiments with linked samples
deseq2 rnaseq repeated measures time series design formula
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
1
vote
1
reply
28k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ★ 1.5k
1
vote
4
replies
929
views
Time series matrix design
deseq2
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 10
0
votes
9
replies
1.8k
views
DESeq2 model matrix question
deseq2
updated 5.9 years ago by ★ 1.4k • written 5.9 years ago by • 0
2
votes
2
replies
1.5k
views
Filtering in DESeq 2 basemean
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
2
replies
1.7k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
5
replies
1.9k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
5.9 years ago omid.alamdari • 0
0
votes
1
reply
1.9k
views
plot statistic values in a DEseq2 plotCounts plot
deseq2 plotCounts pvalues RNAseq
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
vote
2
replies
1.3k
views
Correct DESeq2 interaction design and results with paired and nested data
deseq2 Paired Nested
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
0
votes
2
replies
745
views
multiple group comparison
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
1
vote
7
replies
3.0k
views
DESeq2 namespace load failed for GenomeInfoDb
DESeq2
5.9 years ago Brian Smith ▴ 120
0
votes
4
replies
3.6k
views
How to install older version of DESeq2?
deseq2 software error
updated 5.9 years ago by 25k • written 5.9 years ago by • 0
1
vote
1
reply
502
views
DESeq2: Less significant genes if more samples added?
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
vote
2
replies
591
views
DESeq2 input data.
DESeq2 Normalization Input data
5.9 years ago Fischer-philipp ▴ 30
1
vote
2
replies
2.0k
views
Help understanding the contrast function in DESeq2
deseq2
5.9 years ago Eric de Sousa • 0
1
vote
3
replies
1.2k
views
typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ★ 1.5k
1
vote
1
reply
603
views
Siblings within but not across condition/treatment
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
8
replies
1.6k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
5.9 years ago sara.blocquiaux • 0
1
vote
8
replies
2.0k
views
DESeq2 design matrix: covariates + nested replicates
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
vote
6
replies
939
views
DESeq design matrix, control for contralateral hemisphere
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 60
2
votes
1
reply
1.9k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 5.9 years ago by ▴ 60 • written 5.9 years ago by ★ 1.5k
0
votes
2
replies
704
views
Sample Pairing Design Effects on Dispersion Estimates in DESeq2?
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
1
reply
1.2k
views
Edit: How to analyze matched pairs RNA sequencing data over multiple time points using DESeq2?
deseq2 rnaseq ribotag trap
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
2
replies
543
views
Sequencing machine as fixed effect in DEseq2?
deseq2 edger
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
2
votes
1
reply
745
views
Correlate DESeq2 variance stabilised counts with clinical covariates
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 60
4,840 results • Page 43 of 97
Recent ...
Replies
Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
Popular Question to k___ ▴ 30
Popular Question to efoss ▴ 10
Popular Question to James W. MacDonald 68k
Locations • All
Barcelona, Spain, 52 minutes ago
Germany, 1 hour ago
United States, 2 hours ago
The city by the bay, 3 hours ago
United States, 3 hours ago
Traffic: 847 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6