Showing : DESEQ2 • reset
1
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4
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300
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DESeq2 interactions
DESeq2
written 5 weeks ago by • 0
3
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14
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926
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 12 weeks ago by • 0
0
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2
replies
187
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3-factor DESeq2 trime-series analysis
time-series DESeq2
6 weeks ago gogeni5529 • 0
0
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3
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304
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
0
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1
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543
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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 6 weeks ago by 43k • written 8 weeks ago by • 0
3
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5
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1.0k
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 7 weeks ago by 68k • written 8 weeks ago by ▴ 200
17
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45
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13k
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 8 weeks ago by 68k • written 6.2 years ago by ▴ 60
0
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0
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134
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DESeq2 on non-RNASeq counts data
DESeq2
9 weeks ago vs • 0
1
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10
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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 4 weeks ago by • 0 • written 9 weeks ago by • 0
0
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11
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538
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
10 weeks ago • updated 9 weeks ago Denise • 0
2
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6
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459
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
10 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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230
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 10 weeks ago by ▴ 10
0
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4
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823
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 11 weeks ago by 43k • written 3 months ago by • 0
1
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2
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354
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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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11
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1.9k
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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
3 months ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.5k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
3 months ago bbao ▴ 10
0
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2
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924
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 3 months ago by 68k • written 3 months ago by • 0
0
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1
reply
462
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
0
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2
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941
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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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3.1k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 5 months ago by ▴ 10
1
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5
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4.0k
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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 4 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 4 months ago by 43k • written 4 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 4 months ago by 43k • written 4 months ago by • 0
3
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2
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1.3k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 4 months ago by ▴ 20
1
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2
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2.6k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 4 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 4 months ago by 43k • written 4 months ago by ▴ 10
0
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1
reply
467
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DESeq2 results
result DESeq2 subsetting
updated 4 months ago by ★ 5.0k • written 4 months ago by • 0
0
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1
reply
392
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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
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504
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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
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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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1.3k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
5 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
5 months ago caroline.zanchi ▴ 10
0
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1
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383
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DESeq2 from phyloseq error
DESeq2 phyloseq
5 months ago asafpr • 0
3
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1
reply
599
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 5 months ago by 68k • written 5 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 5 months ago by 68k • written 5 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
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4
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1.7k
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Filtering after DESeq
DESeq2 IHW
written 6 months ago by ▴ 10
0
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4
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1.2k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
5 months ago sk • 0
0
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6
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1.7k
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Discrepancies in normalised count data vs unnormalised
DESeq2
5 months ago AMgroup • 0
0
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2
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672
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Design formula for circadian time-course data for vst() function
DESeq2
6 months ago • updated 5 months ago Vishnu • 0
0
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2
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795
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Analyzing TnSeq data with DESeq2
DESeq2
written 6 months ago by • 0
0
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1
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1.1k
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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
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694
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Differing results with DESeq2
DESeq2
updated 6 months ago by • 0 • written 6 months ago by • 0
0
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2
replies
570
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RNA Seq using Lrt
DESeq2
6 months ago Rob • 0
0
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3
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983
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Log2foldchange strange behavior
DESeq2
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
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1
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865
views
WGCNA
WGCNA DESeq2
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
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1
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1.0k
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by ▴ 20
1
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1
reply
1.3k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 6 months ago by 4.2k • written 6 months ago by • 0
0
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1
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467
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 6 months ago by 68k • written 6 months ago by ▴ 30
4,835 results • Page 1 of 97
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Replies
Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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