Showing : desEQ2 • reset
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2
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Setting up a DESeq2 Design with Paired Data
DESeq2
1 day ago Alexander • 0
2
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4
replies
418
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DESeq2 interactions
DESeq2
updated 10 days ago by 43k • written 7 weeks ago by • 0
3
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14
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1.1k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 3 months ago by • 0
0
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2
replies
220
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3-factor DESeq2 trime-series analysis
time-series DESeq2
8 weeks ago gogeni5529 • 0
0
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3
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340
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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
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5
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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
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0
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147
views
DESeq2 on non-RNASeq counts data
DESeq2
11 weeks ago vs • 0
1
vote
10
replies
1.1k
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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 6 weeks ago by • 0 • written 11 weeks ago by • 0
0
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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
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6
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539
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
12 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
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3
replies
248
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
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13
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2.1k
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
4 months ago • updated 3 months ago bbao ▴ 10
0
votes
2
replies
941
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 4 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
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5
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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
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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
539
views
DESeq2 results
result DESeq2 subsetting
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
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1
reply
404
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 6 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
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3
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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
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2
replies
808
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Analyzing TnSeq data with DESeq2
DESeq2
written 6 months ago by • 0
0
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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
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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
581
views
RNA Seq using Lrt
DESeq2
6 months ago Rob • 0
0
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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 ...
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Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
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, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
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…
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
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