Showing : DESEQ2 • reset
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 3 days ago by 43k • written 4 days ago by • 0
3
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6
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584
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 18 days ago by • 0
0
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1
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112
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 8 days ago by ★ 5.0k • written 9 days ago by • 0
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2
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1.0k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 16 days ago by ★ 4.0k • written 5 months ago by • 0
1
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11
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1.5k
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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 ★ 4.0k • written 3 months ago by • 0
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1
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238
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DESeq2 on non-RNASeq counts data
DESeq2
updated 17 days ago by ★ 4.0k • written 3 months ago by • 0
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2
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300
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 19 days ago by ★ 4.0k • written 12 weeks ago by • 0
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0
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104
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 19 days ago by ★ 4.0k • written 25 days ago by • 0
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4
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192
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
24 days ago • updated 21 days ago Denise • 0
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2
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205
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Setting up a DESeq2 Design with Paired Data
DESeq2
4 weeks ago Alexander • 0
2
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4
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471
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DESeq2 interactions
DESeq2
updated 5 weeks ago by 43k • written 12 weeks ago by • 0
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1.2k
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 4 months ago by • 0
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3
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367
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
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1
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692
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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 3 months ago by 43k • written 3 months ago by • 0
3
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5
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1.1k
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 3 months ago by 68k • written 3 months ago by ▴ 200
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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 3 months ago by 68k • written 6.4 years ago by ▴ 60
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11
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645
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
3 months ago Denise • 0
2
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6
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589
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
3 months ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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281
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 3 months ago by ▴ 10
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4
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880
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
1
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2
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409
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Differential expression on the transcript-level
DESeq2
updated 4 months ago by ★ 1.4k • written 4 months ago by • 0
3
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13
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2.2k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 14 months ago by • 0
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8
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1.9k
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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
4 months ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.6k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
5 months ago • updated 4 months ago bbao ▴ 10
0
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1
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530
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 5 months ago by 68k • written 5 months ago by • 0
0
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2
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993
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gene detection across experiments
DESeq2 Normalization
5 months ago Mara • 0
5
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11
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3.2k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 7 months ago by ▴ 10
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5
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4.6k
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 4 months ago by 43k • written 6 months ago by • 0
1
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1
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2.2k
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 5 months ago by 43k • written 5 months ago by • 0
0
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2
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1.2k
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
3
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2
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1.4k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 6 months ago by ▴ 20
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2
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 6 months ago by • 0
3
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1
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3.8k
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DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 6 months ago by 43k • written 6 months ago by ▴ 10
0
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1
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608
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DESeq2 results
result DESeq2 subsetting
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
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1
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425
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
0
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1
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576
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 6 months ago by 43k • written 7 months ago by • 0
3
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2
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2.1k
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
6 months ago dudutchy ▴ 10
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3
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1.5k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
6 months ago Paulito • 0
4
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4
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2.1k
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Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
6 months ago caroline.zanchi ▴ 10
0
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1
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426
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DESeq2 from phyloseq error
DESeq2 phyloseq
6 months ago asafpr • 0
3
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1
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649
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 6 months ago by 68k • written 6 months ago by • 0
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5
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1.5k
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Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 6 months ago by 68k • written 7 months ago by ▴ 10
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3
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3.1k
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DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 6 months ago by 43k • written 7 months ago by ▴ 40
2
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4
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1.8k
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Filtering after DESeq
DESeq2 IHW
written 7 months ago by ▴ 10
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4
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1.2k
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DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
7 months ago sk • 0
0
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6
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1.8k
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Discrepancies in normalised count data vs unnormalised
DESeq2
7 months ago • updated 6 months ago AMgroup • 0
0
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2
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711
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Design formula for circadian time-course data for vst() function
DESeq2
7 months ago Vishnu • 0
0
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2
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838
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Analyzing TnSeq data with DESeq2
DESeq2
written 7 months ago by • 0
0
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1
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1.2k
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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 7 months ago by 43k • written 8 months ago by • 0
0
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2
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731
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Differing results with DESeq2
DESeq2
updated 7 months ago by • 0 • written 8 months ago by • 0
4,841 results • Page 1 of 97
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
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Popular Question to Gordon Smyth 53k
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