Showing : Deseq2 • reset
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Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 20 days ago by ★ 5.0k • written 20 days ago by • 0
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0
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105
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How to start learning RNA sequence analysis with DESeq2
DESeq2
21 days ago Syed • 0
1
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4
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385
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
22 days ago • updated 21 days ago Mariami • 0
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5
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2.3k
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DESeq2 contrast cleaning problem
software error bugs deseq2
written 10.1 years ago by • 0
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1
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200
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DESeq2 for 16S rRNA Analysis
DESeq2
updated 4 weeks ago by 68k • written 4 weeks ago by • 0
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5
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310
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 5 weeks ago by 43k • written 5 weeks ago by ▴ 10
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2
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259
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lfc shrinkage estimator in DESeq2
DESeq2
written 5 weeks ago by • 0
0
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13
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950
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Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 5 weeks ago by 53k • written 6 weeks ago by • 0
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6
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778
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 6 weeks ago by 25k • written 3 months ago by • 0
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1
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367
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DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 6 weeks ago by ★ 5.0k • written 6 weeks ago by • 0
0
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1
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186
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
written 7 weeks ago by ▴ 20
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3
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499
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
10 weeks ago • updated 6 weeks ago ja569116 • 0
6
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6
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1.2k
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 3 months ago by ▴ 10
0
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1
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290
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 3 months ago by ★ 5.0k • written 3 months ago by • 0
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2
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1.3k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 3 months ago by ★ 4.0k • written 7 months ago by • 0
1
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11
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2.6k
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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 3 months ago by ★ 4.0k • written 6 months ago by • 0
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2
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459
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DESeq2 on non-RNASeq counts data
DESeq2
written 6 months ago by • 0
0
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2
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422
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 3 months ago by ★ 4.0k • written 5 months ago by • 0
0
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1
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290
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
3 months ago • updated 19 days ago colinmccornack • 0
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4
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388
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
3 months ago Denise • 0
0
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2
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462
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Setting up a DESeq2 Design with Paired Data
DESeq2
3 months ago Alexander • 0
2
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4
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636
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DESeq2 interactions
DESeq2
updated 4 months ago by 43k • written 5 months ago by • 0
3
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14
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1.6k
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 7 months ago by • 0
0
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3
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485
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 5 months ago by 43k • written 6 months ago by • 0
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1
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1.0k
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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 5 months ago by 43k • written 6 months ago by • 0
3
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5
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1.3k
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 6 months ago by 68k • written 6 months ago by ▴ 200
17
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45
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14k
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 6 months ago by 68k • written 6.6 years ago by ▴ 60
0
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11
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894
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
6 months ago Denise • 0
2
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6
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728
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago richardallenfriedmanbrooklyn ▴ 30
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3
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411
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 6 months ago by ▴ 10
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4
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1.2k
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
1
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2
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610
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Differential expression on the transcript-level
DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
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13
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2.4k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 17 months ago by • 0
4
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8
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2.2k
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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
7 months ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.9k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago bbao ▴ 10
0
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1
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654
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 7 months ago by 68k • written 7 months ago by • 0
0
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2
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1.1k
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gene detection across experiments
DESeq2 Normalization
8 months ago Mara • 0
5
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11
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4.3k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 10 months ago by ▴ 10
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5
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5.7k
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 7 months ago by 43k • written 8 months ago by • 0
1
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1
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2.3k
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 8 months ago by 43k • written 8 months ago by • 0
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2
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1.3k
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
3
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2
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1.6k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 9 months ago by ▴ 20
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2
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2.8k
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 9 months ago by • 0
3
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1
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3.9k
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DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 8 months ago by 43k • written 9 months ago by ▴ 10
0
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1
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695
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DESeq2 results
result DESeq2 subsetting
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
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1
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520
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
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1
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701
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 9 months ago by 43k • written 9 months ago by • 0
3
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3
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2.3k
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
written 9 months ago by ▴ 10
2
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3
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1.7k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
9 months ago Paulito • 0
4
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4
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2.3k
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Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
9 months ago caroline.zanchi ▴ 10
4,851 results • Page 1 of 98
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Answer: tximeta cannot open annotation gtf? by ATpoint ★ 5.0k
> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Votes
Answer: GSEA error
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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