Showing : Deseq2 • reset
0
votes
0
replies
18
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
10 hours ago chp265 • 0
0
votes
6
replies
510
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 1 day ago by 25k • written 6 weeks ago by • 0
0
votes
1
reply
128
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 17 hours ago by ★ 5.0k • written 4 days ago by • 0
0
votes
0
replies
50
views
News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
8 days ago Frances Turner ▴ 20
0
votes
3
replies
321
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
4 weeks ago • updated 4 days ago ja569116 • 0
3
votes
6
replies
1.0k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 8 weeks ago by • 0
0
votes
1
reply
221
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 7 weeks ago by ★ 5.0k • written 7 weeks ago by • 0
0
votes
2
replies
1.2k
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 8 weeks ago by ★ 4.0k • written 6 months ago by • 0
1
vote
11
replies
2.1k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 8 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
votes
2
replies
356
views
DESeq2 on non-RNASeq counts data
DESeq2
written 5 months ago by • 0
0
votes
2
replies
364
views
3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 9 weeks ago by ★ 4.0k • written 4 months ago by • 0
0
votes
0
replies
170
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
0
votes
4
replies
280
views
Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
9 weeks ago Denise • 0
0
votes
2
replies
297
views
Setting up a DESeq2 Design with Paired Data
DESeq2
10 weeks ago Alexander • 0
2
votes
4
replies
544
views
DESeq2 interactions
DESeq2
updated 11 weeks ago by 43k • written 4 months ago by • 0
3
votes
14
replies
1.3k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 5 months ago by • 0
0
votes
3
replies
412
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
1
reply
790
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 4 months ago by 43k • written 4 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 4 months ago by 68k • written 4 months ago by ▴ 200
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 4 months ago by 68k • written 6.5 years ago by ▴ 60
0
votes
11
replies
752
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
5 months ago Denise • 0
2
votes
6
replies
659
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
3
replies
338
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 5 months ago by ▴ 10
0
votes
4
replies
1.0k
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 5 months ago by 43k • written 6 months ago by • 0
1
vote
2
replies
492
views
Differential expression on the transcript-level
DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
3
votes
13
replies
2.3k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 15 months ago by • 0
4
votes
8
replies
2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
0
votes
1
reply
589
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 6 months ago by 68k • written 6 months ago by • 0
0
votes
2
replies
1.1k
views
gene detection across experiments
DESeq2 Normalization
6 months ago Mara • 0
5
votes
11
replies
3.7k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
1
vote
5
replies
5.1k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 5 months ago by 43k • written 7 months ago by • 0
1
vote
1
reply
2.2k
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 7 months ago by • 0
3
votes
2
replies
1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 7 months ago by ▴ 20
1
vote
2
replies
2.7k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 7 months ago by • 0
3
votes
1
reply
3.8k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 7 months ago by 43k • written 7 months ago by ▴ 10
0
votes
1
reply
652
views
DESeq2 results
result DESeq2 subsetting
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
1
reply
472
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
0
votes
1
reply
632
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 7 months ago by 43k • written 8 months ago by • 0
3
votes
2
replies
2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
8 months ago • updated 7 months ago dudutchy ▴ 10
2
votes
3
replies
1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
4
votes
4
replies
2.1k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
8 months ago • updated 7 months ago caroline.zanchi ▴ 10
0
votes
1
reply
469
views
DESeq2 from phyloseq error
DESeq2 phyloseq
8 months ago asafpr • 0
3
votes
1
reply
695
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 8 months ago by 68k • written 8 months ago by • 0
1
vote
5
replies
1.5k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 8 months ago by 68k • written 8 months ago by ▴ 10
9
votes
3
replies
3.3k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 7 months ago by 43k • written 8 months ago by ▴ 40
2
votes
4
replies
1.9k
views
Filtering after DESeq
DESeq2 IHW
written 9 months ago by ▴ 10
0
votes
4
replies
1.3k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
8 months ago sk • 0
0
votes
6
replies
1.9k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
8 months ago • updated 7 months ago AMgroup • 0
4,845 results • Page 1 of 97
Recent ...
Replies
Answer: Are individual-mouse-based statistics possible in CellChat? by ATpoint ★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
Comment: DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups by ATpoint ★ 5.0k
apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Martin Morgan 25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Awards • All
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to nromerov • 0
Locations • All
Germany, just now
United States, 7 minutes ago
The city by the bay, 12 minutes ago
United States, 33 minutes ago
United States, 57 minutes ago
Traffic: 1492 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