Showing : desEQ2 • reset
0
votes
2
replies
118
views
Setting up a DESeq2 Design with Paired Data
DESeq2
1 day ago • updated 21 hours ago Alexander • 0
2
votes
4
replies
417
views
DESeq2 interactions
DESeq2
updated 10 days ago by 43k • written 7 weeks ago by • 0
3
votes
14
replies
1.1k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 3 months ago by • 0
0
votes
2
replies
220
views
3-factor DESeq2 trime-series analysis
time-series DESeq2
8 weeks ago gogeni5529 • 0
0
votes
3
replies
339
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
0
votes
1
reply
642
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 8 weeks ago by 43k • written 10 weeks ago by • 0
3
votes
5
replies
1.1k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 9 weeks ago by 68k • written 10 weeks ago by ▴ 200
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 10 weeks ago by 68k • written 6.3 years ago by ▴ 60
0
votes
0
replies
147
views
DESeq2 on non-RNASeq counts data
DESeq2
11 weeks ago vs • 0
1
vote
10
replies
1.1k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 6 weeks ago by • 0 • written 11 weeks ago by • 0
0
votes
11
replies
585
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
12 weeks ago • updated 11 weeks ago Denise • 0
2
votes
6
replies
539
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
12 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
votes
3
replies
247
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 12 weeks ago by ▴ 10
0
votes
4
replies
839
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
vote
2
replies
391
views
Differential expression on the transcript-level
DESeq2
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
3
votes
13
replies
2.0k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 13 months ago by • 0
4
votes
8
replies
1.8k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
3 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.6k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
3 months ago bbao ▴ 10
0
votes
2
replies
941
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 3 months ago by 68k • written 4 months ago by • 0
0
votes
1
reply
501
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 4 months ago by 68k • written 4 months ago by • 0
0
votes
2
replies
954
views
gene detection across experiments
DESeq2 Normalization
4 months ago Mara • 0
5
votes
11
replies
3.2k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 6 months ago by ▴ 10
1
vote
5
replies
4.2k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 3 months ago by 43k • written 5 months ago by • 0
1
vote
1
reply
2.1k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
2
replies
1.1k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
3
votes
2
replies
1.4k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 5 months ago by ▴ 20
1
vote
2
replies
2.6k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 5 months ago by • 0
3
votes
1
reply
3.7k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 5 months ago by 43k • written 5 months ago by ▴ 10
0
votes
1
reply
538
views
DESeq2 results
result DESeq2 subsetting
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
votes
1
reply
403
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
1
reply
546
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 5 months ago by • 0
3
votes
2
replies
2.0k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
5 months ago dudutchy ▴ 10
2
votes
3
replies
1.4k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
5 months ago Paulito • 0
4
votes
4
replies
2.0k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
5 months ago caroline.zanchi ▴ 10
0
votes
1
reply
394
views
DESeq2 from phyloseq error
DESeq2 phyloseq
5 months ago asafpr • 0
3
votes
1
reply
616
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 5 months ago by 68k • written 5 months ago by • 0
1
vote
5
replies
1.4k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 5 months ago by 68k • written 5 months ago by ▴ 10
8
votes
3
replies
3.0k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 5 months ago by 43k • written 6 months ago by ▴ 40
2
votes
4
replies
1.8k
views
Filtering after DESeq
DESeq2 IHW
written 6 months ago by ▴ 10
0
votes
4
replies
1.2k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
6 months ago sk • 0
0
votes
6
replies
1.7k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
6 months ago • updated 5 months ago AMgroup • 0
0
votes
2
replies
677
views
Design formula for circadian time-course data for vst() function
DESeq2
6 months ago Vishnu • 0
0
votes
2
replies
808
views
Analyzing TnSeq data with DESeq2
DESeq2
written 6 months ago by • 0
0
votes
1
reply
1.2k
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 6 months ago by 43k • written 7 months ago by • 0
0
votes
2
replies
706
views
Differing results with DESeq2
DESeq2
updated 6 months ago by • 0 • written 7 months ago by • 0
0
votes
2
replies
580
views
RNA Seq using Lrt
DESeq2
6 months ago Rob • 0
0
votes
3
replies
1.0k
views
Log2foldchange strange behavior
DESeq2
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
votes
1
reply
880
views
WGCNA
WGCNA DESeq2
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
1
reply
1.1k
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by ▴ 20
1
vote
1
reply
1.3k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 7 months ago by 4.2k • written 7 months ago by • 0
4,836 results • Page 1 of 97
Recent ...
Replies
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi bioinffun, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to …
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be f…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
Awards • All
Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
Popular Question to edward.esiribloom • 0
Locations • All
United States, just now
Russia, 44 minutes ago
Finland, 1 hour ago
The Cave, 181 Longwood Avenue, Boston, USA, 1 hour ago
Seattle, WA, United States, 3 hours ago
Traffic: 851 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