Showing : deseq2 • reset
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152
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Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 12 days ago by ★ 5.0k • written 12 days ago by • 0
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0
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88
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How to start learning RNA sequence analysis with DESeq2
DESeq2
13 days ago Syed • 0
1
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4
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331
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
14 days ago • updated 13 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
0
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1
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188
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DESeq2 for 16S rRNA Analysis
DESeq2
updated 24 days ago by 68k • written 24 days ago by • 0
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5
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298
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 27 days ago by 43k • written 27 days ago by • 0
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2
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242
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lfc shrinkage estimator in DESeq2
DESeq2
written 28 days ago by • 0
0
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13
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909
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Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 28 days ago by 53k • written 4 weeks ago by • 0
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6
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718
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 4 weeks ago by 25k • written 11 weeks ago by • 0
0
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1
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330
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DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 4 weeks ago by ★ 5.0k • written 5 weeks ago by • 0
0
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1
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175
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
written 6 weeks ago by ▴ 20
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3
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461
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
9 weeks ago • updated 5 weeks ago ja569116 • 0
3
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6
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1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 3 months ago by • 0
0
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1
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265
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 12 weeks ago by ★ 5.0k • written 12 weeks 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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2.4k
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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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439
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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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407
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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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266
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
3 months ago • updated 11 days ago colinmccornack • 0
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4
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365
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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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428
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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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618
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DESeq2 interactions
DESeq2
updated 3 months ago by 43k • written 5 months ago by • 0
3
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14
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1.5k
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 6 months ago by • 0
0
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3
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462
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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 5 months ago by • 0
0
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1
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983
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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 5 months ago by 68k • written 6 months ago by ▴ 200
17
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45
replies
14k
views
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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850
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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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708
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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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384
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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 6 months ago by 43k • written 7 months ago by • 0
1
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2
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585
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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 16 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
7
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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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635
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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
7 months ago Mara • 0
5
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11
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4.2k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 9 months ago by ▴ 10
1
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5
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5.6k
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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
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 8 months ago by ▴ 20
1
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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 8 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 8 months ago by ▴ 10
0
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1
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686
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DESeq2 results
result DESeq2 subsetting
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
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1
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509
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
0
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1
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686
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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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2.2k
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
written 9 months ago by ▴ 10
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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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Replies
Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts by a2a2hset32aa • 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
Votes
Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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Popular Question to Dario Strbenac ★ 1.6k
Popular Question to chirag.parsania ▴ 10
Popular Question to Michael Love 43k
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Scholar to Gordon Smyth 53k
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