Showing : DESeq2 • reset
1
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4
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240
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DESeq2 interactions
DESeq2
written 18 days ago by • 0
3
votes
14
replies
865
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 9 weeks ago by • 0
0
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2
replies
154
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3-factor DESeq2 trime-series analysis
time-series DESeq2
22 days ago • updated 21 days ago gogeni5529 • 0
0
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3
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264
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 21 days ago by 43k • written 4 weeks ago by • 0
0
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1
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354
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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 24 days ago by 43k • written 5 weeks ago by • 0
3
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5
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995
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 4 weeks ago by 68k • written 5 weeks 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 5 weeks ago by 68k • written 6.2 years ago by ▴ 60
0
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0
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122
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DESeq2 on non-RNASeq counts data
DESeq2
6 weeks ago vs • 0
1
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10
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1.0k
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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
updated 7 days ago by • 0 • written 6 weeks ago by • 0
0
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11
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498
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
6 weeks ago Denise • 0
2
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6
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424
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
7 weeks ago • updated 6 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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210
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 7 weeks ago by ▴ 10
0
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4
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793
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 8 weeks ago by 43k • written 11 weeks ago by • 0
1
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2
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342
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Differential expression on the transcript-level
DESeq2
updated 9 weeks ago by ★ 1.4k • written 9 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 12 months ago by • 0
4
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8
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1.8k
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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
11 weeks ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.4k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
11 weeks ago bbao ▴ 10
0
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2
replies
911
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 11 weeks ago by 68k • written 12 weeks ago by • 0
0
votes
1
reply
444
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
0
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2
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914
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gene detection across experiments
DESeq2 Normalization
3 months ago Mara • 0
5
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11
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3.0k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 5 months ago by ▴ 10
1
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5
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3.8k
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 9 weeks ago by 43k • written 3 months ago by • 0
1
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1
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2.1k
views
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
votes
2
replies
1.3k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 3 months ago by ▴ 20
1
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2
replies
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 4 months ago by ▴ 10
0
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1
reply
448
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DESeq2 results
result DESeq2 subsetting
updated 4 months ago by ★ 4.9k • written 4 months ago by • 0
0
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1
reply
372
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
0
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1
reply
477
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 4 months ago by 43k • written 4 months ago by • 0
3
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2
replies
2.0k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
4 months ago dudutchy ▴ 10
2
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3
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1.3k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
4 months ago Paulito • 0
4
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4
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2.0k
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Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
4 months ago caroline.zanchi ▴ 10
0
votes
1
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372
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DESeq2 from phyloseq error
DESeq2 phyloseq
4 months ago asafpr • 0
3
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1
reply
571
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
replies
1.3k
views
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 4 months ago by 43k • written 5 months ago by ▴ 40
2
votes
4
replies
1.6k
views
Filtering after DESeq
DESeq2 IHW
written 5 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
5 months ago • updated 4 months ago sk • 0
0
votes
6
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1.7k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
5 months ago • updated 4 months ago AMgroup • 0
0
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2
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652
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Design formula for circadian time-course data for vst() function
DESeq2
5 months ago Vishnu • 0
0
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2
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782
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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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680
views
Differing results with DESeq2
DESeq2
updated 5 months ago by • 0 • written 6 months ago by • 0
0
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2
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550
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RNA Seq using Lrt
DESeq2
5 months ago Rob • 0
0
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3
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962
views
Log2foldchange strange behavior
DESeq2
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
0
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1
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846
views
WGCNA
WGCNA DESeq2
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
0
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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
461
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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
Recent ...
Replies
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
Comment: Sharing a collection of datasets in ExperimentHub by Peter Hickey ▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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