Showing : Deseq2 • reset
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Subsetting DDS object for individual conditions over time
DESeq2
1 day ago • updated 10 hours ago A ▴ 60
1
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1
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236
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Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 23 days ago by ★ 5.0k • written 23 days ago by • 0
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0
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109
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How to start learning RNA sequence analysis with DESeq2
DESeq2
24 days ago Syed • 0
1
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4
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410
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
25 days ago • updated 24 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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203
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DESeq2 for 16S rRNA Analysis
DESeq2
updated 5 weeks ago by 68k • written 5 weeks ago by • 0
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5
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312
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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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263
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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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967
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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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789
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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
0
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1
reply
380
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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 7 weeks ago by • 0
0
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1
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197
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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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514
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
11 weeks ago • updated 7 weeks ago ja569116 • 0
6
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6
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1.3k
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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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293
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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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2.7k
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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
0
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2
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467
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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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424
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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
reply
292
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
3 months ago • updated 22 days ago colinmccornack • 0
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4
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394
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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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483
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Setting up a DESeq2 Design with Paired Data
DESeq2
4 months ago • updated 3 months ago Alexander • 0
2
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4
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651
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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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489
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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
0
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1
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1.1k
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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
views
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
votes
45
replies
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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903
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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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737
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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419
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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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620
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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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6.0k
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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
reply
658
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 7 months ago by 68k • written 8 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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4.4k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 10 months ago by ▴ 10
1
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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 9 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
0
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2
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1.4k
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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 9 months ago by 43k • written 9 months ago by ▴ 10
0
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1
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696
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DESeq2 results
result DESeq2 subsetting
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
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1
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527
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
0
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1
reply
703
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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
4,852 results • Page 1 of 98
Recent ...
Replies
Comment: Subsetting DDS object for individual conditions over time by A ▴ 60
Hi @atpoint Thank you for the quick reply! and this makes sense! I will confirm with a corr to see how the SFs differ but also how DE dif…
Answer: Subsetting DDS object for individual conditions over time by ATpoint ★ 5.0k
It would surprise my quite a bit if the size factors would differ notably between subset or not. I would always try to keep the size factor…
Comment: GSEA error by Adithi • 0
Thank you so much. That makes perfect sense to me. I will work on this.
Comment: tximeta cannot open annotation gtf? by Michael Love 43k
Yes, so this is the same type of error you would get if you tried to assemble a *SummarizedExperiment* manually with tximport + GTF process…
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…
Votes
Answer: RNA Seq using Lrt
Answer: DESeq2 LRT Reduced Formula
Answer: DESeq2: LRT or WALD guidance
Answer: GSEA error
Answer: OrgDb for maize
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