Showing : DESeq2 • reset
1
vote
1
reply
101
views
Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 2 days ago by ★ 5.0k • written 2 days ago by • 0
0
votes
0
replies
67
views
How to start learning RNA sequence analysis with DESeq2
DESeq2
3 days ago Syed • 0
1
vote
4
replies
283
views
Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
4 days ago • updated 3 days ago Mariami • 0
0
votes
5
replies
2.3k
views
DESeq2 contrast cleaning problem
software error bugs deseq2
written 10.0 years ago by • 0
0
votes
1
reply
166
views
DESeq2 for 16S rRNA Analysis
DESeq2
updated 14 days ago by 68k • written 15 days ago by • 0
0
votes
5
replies
278
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 17 days ago by 43k • written 17 days ago by • 0
0
votes
2
replies
214
views
lfc shrinkage estimator in DESeq2
DESeq2
written 18 days ago by • 0
0
votes
13
replies
866
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 18 days ago by 53k • written 24 days ago by • 0
0
votes
6
replies
665
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 25 days ago by 25k • written 10 weeks ago by • 0
0
votes
1
reply
305
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 24 days ago by ★ 5.0k • written 28 days ago by • 0
0
votes
1
reply
155
views
News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
written 4 weeks ago by ▴ 20
0
votes
3
replies
426
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
8 weeks ago • updated 28 days ago ja569116 • 0
3
votes
6
replies
1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 12 weeks ago by • 0
0
votes
1
reply
255
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 10 weeks ago by ★ 5.0k • written 10 weeks ago by • 0
0
votes
2
replies
1.3k
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 12 weeks ago by ★ 4.0k • written 7 months ago by • 0
1
vote
11
replies
2.4k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 12 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
votes
2
replies
415
views
DESeq2 on non-RNASeq counts data
DESeq2
written 5 months ago by • 0
0
votes
2
replies
398
views
3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 12 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
votes
1
reply
239
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
3 months ago • updated 1 day ago colinmccornack • 0
0
votes
4
replies
348
views
Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
3 months ago • updated 12 weeks ago Denise • 0
0
votes
2
replies
402
views
Setting up a DESeq2 Design with Paired Data
DESeq2
3 months ago Alexander • 0
2
votes
4
replies
594
views
DESeq2 interactions
DESeq2
updated 3 months ago by 43k • written 5 months ago by • 0
3
votes
14
replies
1.5k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 6 months ago by • 0
0
votes
3
replies
448
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
1
reply
913
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
3
votes
5
replies
1.2k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 5 months ago by 68k • written 5 months ago by ▴ 200
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 5 months ago by 68k • written 6.6 years ago by ▴ 60
0
votes
11
replies
831
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
6 months ago • updated 5 months ago Denise • 0
2
votes
6
replies
695
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
3
replies
368
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 6 months ago by ▴ 10
0
votes
4
replies
1.1k
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 6 months ago by 43k • written 7 months ago by • 0
1
vote
2
replies
560
views
Differential expression on the transcript-level
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
3
votes
13
replies
2.4k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
4
votes
8
replies
2.1k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
7 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.9k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago bbao ▴ 10
0
votes
1
reply
617
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 7 months ago by 68k • written 7 months ago by • 0
0
votes
2
replies
1.1k
views
gene detection across experiments
DESeq2 Normalization
7 months ago Mara • 0
5
votes
11
replies
4.1k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 9 months ago by ▴ 10
1
vote
5
replies
5.4k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 6 months ago by 43k • written 8 months ago by • 0
1
vote
1
reply
2.3k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 7 months ago by 43k • written 7 months ago by • 0
0
votes
2
replies
1.3k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 7 months ago by 43k • written 8 months ago by • 0
3
votes
2
replies
1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
1
vote
2
replies
2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 8 months ago by • 0
3
votes
1
reply
3.9k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 8 months ago by 43k • written 8 months ago by ▴ 10
0
votes
1
reply
685
views
DESeq2 results
result DESeq2 subsetting
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
votes
1
reply
503
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
673
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 8 months ago by 43k • written 9 months ago by • 0
3
votes
3
replies
2.2k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
updated 2 days ago by • 0 • written 9 months ago by ▴ 10
2
votes
3
replies
1.7k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
4
votes
4
replies
2.2k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
8 months ago caroline.zanchi ▴ 10
4,851 results • Page 1 of 98
Recent ...
Replies
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Subsetting data verses contrasts [DESeq2]?
A: WGCNA differences two groups 10 replicates each group
A: WGCNA sample size minimum: why?
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
Answer: Can you colour dendrogram branch clusters in pheatmap?
Awards • All
Popular Question to Peter Hickey &utrif; 760
Popular Question to Sean Davis 21k
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.3k
Popular Question to Andreas Zankl &utrif; 80
Locations • All
WEHI, Melbourne, Australia, 3 minutes ago
The city by the bay, 18 minutes ago
United States, 2 hours ago
United States, 8 hours ago
United States, 9 hours ago
Traffic: 784 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats
See More

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

Powered by the version 2.3.6