Showing : DEseq2 • reset
2
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4
replies
344
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DESeq2 interactions
DESeq2
updated 2 days ago by 43k • written 6 weeks ago by • 0
3
votes
14
replies
969
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 3 months ago by • 0
0
votes
2
replies
194
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3-factor DESeq2 trime-series analysis
time-series DESeq2
7 weeks ago gogeni5529 • 0
0
votes
3
replies
316
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 7 weeks ago by 43k • written 8 weeks ago by • 0
0
votes
1
reply
617
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 7 weeks ago by 43k • written 9 weeks ago by • 0
3
votes
5
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1.0k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 8 weeks ago by 68k • written 9 weeks ago by ▴ 200
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 9 weeks ago by 68k • written 6.3 years ago by ▴ 60
0
votes
0
replies
138
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DESeq2 on non-RNASeq counts data
DESeq2
10 weeks ago vs • 0
1
vote
10
replies
1.1k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 5 weeks ago by • 0 • written 10 weeks ago by • 0
0
votes
11
replies
558
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
10 weeks ago Denise • 0
2
votes
6
replies
495
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
11 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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235
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 11 weeks ago by ▴ 10
0
votes
4
replies
826
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
1
vote
2
replies
370
views
Differential expression on the transcript-level
DESeq2
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
3
votes
11
replies
2.0k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 12 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
5.5k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
3 months ago bbao ▴ 10
0
votes
2
replies
930
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 3 months ago by 68k • written 3 months ago by • 0
0
votes
1
reply
481
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
votes
2
replies
948
views
gene detection across experiments
DESeq2 Normalization
4 months ago Mara • 0
5
votes
11
replies
3.1k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 6 months ago by ▴ 10
1
vote
5
replies
4.0k
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 4 months ago by • 0
1
vote
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 4 months ago by ▴ 20
1
vote
2
replies
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
votes
1
reply
497
views
DESeq2 results
result DESeq2 subsetting
updated 4 months ago by ★ 5.0k • written 4 months ago by • 0
0
votes
1
reply
397
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
1
reply
524
views
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
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
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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
386
views
DESeq2 from phyloseq error
DESeq2 phyloseq
5 months ago asafpr • 0
3
votes
1
reply
604
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
1.3k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 5 months ago by 68k • written 5 months ago by ▴ 10
8
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 5 months ago by ▴ 40
2
votes
4
replies
1.7k
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 • updated 5 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
673
views
Design formula for circadian time-course data for vst() function
DESeq2
6 months ago Vishnu • 0
0
votes
2
replies
798
views
Analyzing TnSeq data with DESeq2
DESeq2
written 6 months ago by • 0
0
votes
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
votes
2
replies
696
views
Differing results with DESeq2
DESeq2
updated 6 months ago by • 0 • written 7 months ago by • 0
0
votes
2
replies
573
views
RNA Seq using Lrt
DESeq2
6 months ago Rob • 0
0
votes
3
replies
992
views
Log2foldchange strange behavior
DESeq2
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
votes
1
reply
871
views
WGCNA
WGCNA DESeq2
updated 6 months ago by ★ 5.0k • written 6 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 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
reply
471
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: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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