Showing : DEseq2 • reset
1
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DESeq2 interactions
DESeq2
updated 6 days ago by ★ 1.4k • written 7 days ago by • 0
3
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14
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797
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 7 weeks ago by • 0
0
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2
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132
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3-factor DESeq2 trime-series analysis
time-series DESeq2
11 days ago • updated 10 days ago gogeni5529 • 0
0
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3
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236
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 10 days ago by 43k • written 19 days ago by • 0
0
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1
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228
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Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 13 days ago by 43k • written 27 days ago by • 0
3
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5
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963
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 19 days ago by 68k • written 25 days ago by ▴ 200
17
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45
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12k
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 26 days ago by 68k • written 6.2 years ago by ▴ 60
0
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0
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96
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DESeq2 on non-RNASeq counts data
DESeq2
4 weeks ago vs • 0
1
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9
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799
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Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
4 weeks ago Raya • 0
0
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11
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457
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
5 weeks ago • updated 4 weeks ago Denise • 0
2
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6
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403
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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192
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 5 weeks ago by ▴ 10
0
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4
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782
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 6 weeks ago by 43k • written 9 weeks ago by • 0
1
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2
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333
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Differential expression on the transcript-level
DESeq2
updated 7 weeks ago by ★ 1.4k • written 8 weeks ago by • 0
3
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11
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1.9k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 11 months ago by • 0
4
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8
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1.7k
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
10 weeks ago • updated 9 weeks ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.4k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
10 weeks ago • updated 9 weeks ago bbao ▴ 10
0
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2
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904
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 10 weeks ago by 68k • written 10 weeks ago by • 0
0
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1
reply
433
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 10 weeks ago by 68k • written 10 weeks ago by • 0
0
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2
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898
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gene detection across experiments
DESeq2 Normalization
12 weeks ago • updated 11 weeks ago Mara • 0
5
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11
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3.0k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 4 months ago by ▴ 10
1
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5
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3.7k
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 8 weeks ago by 43k • written 3 months ago by • 0
1
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1
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2.1k
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 3 months ago by 43k • written 3 months ago by • 0
0
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2
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1.1k
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
3
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2
replies
1.3k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 3 months ago by ▴ 20
1
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2
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2.5k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 3 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 3 months ago by 43k • written 3 months ago by ▴ 10
0
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1
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442
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DESeq2 results
result DESeq2 subsetting
updated 3 months ago by ★ 4.9k • written 3 months ago by • 0
0
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1
reply
361
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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1
reply
463
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 3 months ago by 43k • written 4 months ago by • 0
3
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2
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2.0k
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
4 months ago • updated 3 months ago dudutchy ▴ 10
2
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3
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1.2k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
4 months ago • updated 3 months ago Paulito • 0
4
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4
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2.0k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
4 months ago • updated 3 months ago caroline.zanchi ▴ 10
0
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1
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364
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DESeq2 from phyloseq error
DESeq2 phyloseq
4 months ago asafpr • 0
3
votes
1
reply
556
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 4 months ago by 68k • written 4 months ago by • 0
1
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5
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1.3k
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Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 4 months ago by 68k • written 4 months ago by ▴ 10
8
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3
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3.0k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 3 months ago by 43k • written 4 months ago by ▴ 40
2
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4
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1.6k
views
Filtering after DESeq
DESeq2 IHW
written 4 months ago by ▴ 10
0
votes
4
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1.2k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
4 months ago sk • 0
0
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6
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1.7k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
4 months ago • updated 3 months ago AMgroup • 0
0
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2
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634
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Design formula for circadian time-course data for vst() function
DESeq2
4 months ago Vishnu • 0
0
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2
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773
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Analyzing TnSeq data with DESeq2
DESeq2
written 5 months ago by • 0
0
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1
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1.1k
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 5 months ago by 43k • written 6 months ago by • 0
0
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2
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665
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Differing results with DESeq2
DESeq2
updated 5 months ago by • 0 • written 5 months ago by • 0
0
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2
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541
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RNA Seq using Lrt
DESeq2
5 months ago Rob • 0
0
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3
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944
views
Log2foldchange strange behavior
DESeq2
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
0
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1
reply
836
views
WGCNA
WGCNA DESeq2
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
0
votes
1
reply
1.0k
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by ▴ 20
1
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1
reply
1.3k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 5 months ago by 4.2k • written 5 months ago by • 0
0
votes
1
reply
450
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 5 months ago by 68k • written 5 months ago by ▴ 30
4,835 results • Page 1 of 97
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Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexecutor4 • 0
FFH4X is a [Free Fire mod][1] menu APK that offers cheats like auto headshot, aimbot, ESP, wallhack, and unlimited skins. Players use it to…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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