Showing : deseq2 • reset
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 10 days ago by 43k • written 11 days ago by • 0
3
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6
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708
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 25 days ago by • 0
0
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1
reply
137
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 15 days ago by ★ 5.0k • written 16 days ago by • 0
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2
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1.1k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 24 days ago by ★ 4.0k • written 5 months ago by • 0
1
vote
11
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1.6k
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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 24 days ago by ★ 4.0k • written 3 months ago by • 0
0
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1
reply
258
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DESeq2 on non-RNASeq counts data
DESeq2
updated 25 days ago by ★ 4.0k • written 3 months ago by • 0
0
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2
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327
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 27 days ago by ★ 4.0k • written 3 months ago by • 0
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0
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118
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 27 days ago by ★ 4.0k • written 4 weeks ago by • 0
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4
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213
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
4 weeks ago • updated 28 days ago Denise • 0
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2
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220
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Setting up a DESeq2 Design with Paired Data
DESeq2
5 weeks ago Alexander • 0
2
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4
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480
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DESeq2 interactions
DESeq2
updated 6 weeks ago by 43k • written 3 months ago by • 0
3
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14
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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
0
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3
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373
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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1
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700
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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
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 3 months ago by 68k • written 6.4 years ago by ▴ 60
0
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11
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674
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
4 months ago • updated 3 months ago Denise • 0
2
votes
6
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607
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
4 months ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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293
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 4 months ago by ▴ 10
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4
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888
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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 5 months ago by • 0
1
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2
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418
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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
4
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8
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1.9k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
5 months ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.7k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
5 months ago bbao ▴ 10
0
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1
reply
539
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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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1.0k
views
gene detection across experiments
DESeq2 Normalization
5 months ago Mara • 0
5
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11
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3.3k
views
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 6 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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2.7k
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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
reply
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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615
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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
reply
434
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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
reply
589
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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
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
7 months ago • updated 6 months ago dudutchy ▴ 10
2
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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
views
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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431
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DESeq2 from phyloseq error
DESeq2 phyloseq
7 months ago asafpr • 0
3
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1
reply
652
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 7 months ago by 68k • written 7 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 7 months ago by 68k • written 7 months ago by ▴ 10
8
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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
0
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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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723
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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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854
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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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741
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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
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Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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…
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
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