Showing : DEseq2 • reset
1
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DESeq2 interactions
DESeq2
written 26 days ago by • 0
3
votes
14
replies
889
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 10 weeks ago by • 0
0
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2
replies
165
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3-factor DESeq2 trime-series analysis
time-series DESeq2
4 weeks ago • updated 29 days ago gogeni5529 • 0
0
votes
3
replies
280
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 29 days ago by 43k • written 5 weeks ago by • 0
0
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1
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432
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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 4 weeks ago by 43k • written 6 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 5 weeks ago by 68k • written 6 weeks ago by ▴ 200
17
votes
45
replies
12k
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 6 weeks ago by 68k • written 6.2 years ago by ▴ 60
0
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0
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126
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DESeq2 on non-RNASeq counts data
DESeq2
7 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 16 days ago by • 0 • written 7 weeks ago by • 0
0
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11
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516
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
7 weeks ago Denise • 0
2
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6
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433
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
8 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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215
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 8 weeks ago by ▴ 10
0
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4
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805
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 9 weeks ago by 43k • written 12 weeks ago by • 0
1
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2
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345
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Differential expression on the transcript-level
DESeq2
updated 10 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
3
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11
replies
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
12 weeks ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.4k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
3 months ago • updated 12 weeks ago bbao ▴ 10
0
votes
2
replies
912
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
447
views
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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920
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gene detection across experiments
DESeq2 Normalization
3 months ago Mara • 0
5
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11
replies
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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3.9k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 11 weeks 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 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
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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
replies
2.5k
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
votes
1
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453
views
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
379
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
1
reply
486
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 4 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 • updated 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
views
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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374
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DESeq2 from phyloseq error
DESeq2 phyloseq
4 months ago asafpr • 0
3
votes
1
reply
580
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
replies
1.3k
views
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
replies
1.6k
views
Filtering after DESeq
DESeq2 IHW
written 5 months ago by ▴ 10
0
votes
4
replies
1.2k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
5 months ago sk • 0
0
votes
6
replies
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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659
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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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787
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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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686
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Differing results with DESeq2
DESeq2
updated 5 months ago by • 0 • written 6 months ago by • 0
0
votes
2
replies
557
views
RNA Seq using Lrt
DESeq2
5 months ago Rob • 0
0
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3
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963
views
Log2foldchange strange behavior
DESeq2
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
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1
reply
850
views
WGCNA
WGCNA DESeq2
updated 6 months ago by ★ 5.0k • written 6 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 6 months ago by ★ 1.4k • written 6 months ago by ▴ 20
1
vote
1
reply
1.3k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 6 months ago by 4.2k • written 6 months ago by • 0
0
votes
1
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462
views
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
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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