Showing : DESeq2 • reset
38
votes
23
replies
18k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
11.4 years ago • updated 10 months ago Michael Love 43k
31
votes
25
replies
63k
views
deseq2 filter the low counts
deseq2 lowcount
updated 12 weeks ago by 43k • written 10.9 years ago by ▴ 40
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 4 months ago by 68k • written 6.5 years ago by ▴ 60
12
votes
7
replies
23k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2 multiple factor design
updated 8 months ago by ▴ 740 • written 10.7 years ago by ▴ 50
9
votes
15
replies
7.5k
views
DESeq2 on NanoString Data
deseq2 nanostring
updated 4 months ago by 43k • written 7.6 years ago by ▴ 170
9
votes
3
replies
3.3k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 7 months ago by 43k • written 8 months ago by ▴ 40
8
votes
10
replies
18k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 8 months ago by ★ 5.0k • written 9.5 years ago by ▴ 20
7
votes
9
replies
5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
6
votes
4
replies
8.2k
views
DESeq2 with proteomics data
deseq2
updated 8 months ago by • 0 • written 7.5 years ago by ▴ 10
5
votes
30
replies
6.8k
views
DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2 multiple time points time course casecontrol model design
updated 9 months ago by • 0 • written 8.6 years ago by ▴ 10
5
votes
3
replies
29k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 7.0 years ago by ▴ 30
5
votes
11
replies
3.7k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
5
votes
4
replies
2.8k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
updated 11 months ago by • 0 • written 3.7 years ago by ▴ 30
5
votes
5
replies
4.0k
views
Cannot extract size factor from DESeq2 analysis
deseq2 tximport
updated 7 months ago by 43k • written 5.7 years ago by • 0
4
votes
6
replies
1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
4
votes
4
replies
2.2k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
8 months ago caroline.zanchi ▴ 10
4
votes
8
replies
2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
14
replies
1.3k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 5 months ago by • 0
3
votes
5
replies
1.2k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 4 months ago by 68k • written 4 months ago by ▴ 200
3
votes
6
replies
1.0k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 9 weeks ago by • 0
3
votes
13
replies
2.3k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 15 months ago by • 0
3
votes
2
replies
1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 7 months ago by ▴ 20
3
votes
2
replies
2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
8 months ago • updated 7 months ago dudutchy ▴ 10
3
votes
1
reply
696
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 8 months ago by 68k • written 8 months ago by • 0
3
votes
7
replies
2.5k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 10 months ago by ▴ 10 • written 6.9 years ago by ▴ 20
3
votes
1
reply
3.9k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 7 months ago by 43k • written 7 months ago by ▴ 10
2
votes
6
replies
2.6k
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 10 months ago by • 0 • written 20 months ago by • 0
2
votes
4
replies
1.9k
views
Filtering after DESeq
DESeq2 IHW
written 9 months ago by ▴ 10
2
votes
2
replies
915
views
Plot title for PCA in DESeq2
DESeq2
11 months ago AL • 0
2
votes
5
replies
901
views
Joining different datasets and analyzing using the group-specific condition effects strategy (DESeq2)
DESeq2
updated 8 days ago by 68k • written 3.0 years ago by • 0
2
votes
3
replies
1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
2
votes
6
replies
666
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 months ago richardallenfriedmanbrooklyn ▴ 30
2
votes
5
replies
1.5k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
11 months ago • updated 10 months ago picasa1983 • 0
2
votes
4
replies
2.5k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 10 months ago by 43k • written 3.6 years ago by ▴ 10
2
votes
2
replies
756
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
2
votes
3
replies
2.7k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 9 months ago by • 0 • written 3.3 years ago by ▴ 50
2
votes
4
replies
549
views
DESeq2 interactions
DESeq2
updated 12 weeks ago by 43k • written 4 months ago by • 0
1
vote
3
replies
6.2k
views
DESeq2 estimateSizeFactors with control genes
deseq2 differential gene expression controls references
updated 10 months ago by • 0 • written 7.2 years ago by • 0
1
vote
1
reply
1.4k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 9 months ago by 4.3k • written 9 months ago by • 0
1
vote
2
replies
2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 7 months ago by • 0
1
vote
4
replies
2.8k
views
Pairwise comparison of multiple groups with different base
deseq2 rna-seq r
updated 4 days ago by • 0 • written 5.7 years ago by ▴ 10
1
vote
6
replies
2.2k
views
how to analysis htseq-count
deseq2
written 8.0 years ago by ▴ 30
1
vote
5
replies
2.1k
views
p-value the same for different contrasts DESeq2
deseq2 design and contrast matrix
updated 11 months ago by ▴ 10 • written 7.7 years ago by ▴ 10
1
vote
5
replies
4.7k
views
DESeq2 swap ensembl gene id rownames with gene symbol column
deseq2 dataframe ensembl gene id gene symbol entrezid
updated 10 months ago by • 0 • written 6.1 years ago by ▴ 10
1
vote
2
replies
1.4k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
1
vote
11
replies
2.1k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 8 weeks ago by ★ 4.0k • written 5 months ago by • 0
1
vote
2
replies
930
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ▴ 10 • written 2.1 years ago by • 0
1
vote
1
reply
729
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 10
1
vote
10
replies
11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 6 months ago by 43k • written 6.2 years ago by • 0
1
vote
2
replies
2.9k
views
selecting result from deseq2
DESeq2
updated 4 months ago by 43k • written 5.8 years ago by • 0
124 results • Page 1 of 3
Recent ...
Replies
Answer: Bile acid analysis with limpa by Gordon Smyth 53k
I am not familiar with targeted HPLC-MS and I don't know what you mean by "peak areas". If it produces standard mass spec data, then limpa …
Comment: How to convert .raw data for use in xcms by TikTsossa33ssalpc • 0
It sounds like your mzML conversion has a CV term that XCMS doesn t recognize, which often happens with newer vendor formats or outdated ms…
Comment: Boolean Gate Combination for Any 2 Positive Events in flowWorkspace by TikTsossa33ssalpc • 0
To calculate event numbers for boolean combinations in flow cytometry, you should use a logic gating tool or a script that processes popula…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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