Showing : deseq • reset
8
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4
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2.6k
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DESeq2: interaction term as in limma
deseq2 deseq limma interaction term
updated 8.4 years ago by ★ 3.8k • written 8.4 years ago by ▴ 80
5
votes
2
replies
1.8k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq deseq2 vst
updated 8.4 years ago by ★ 13k • written 8.4 years ago by • 0
4
votes
14
replies
22k
views
standard error value (lfcSE) returned by DeSeq2
deseq2 deseq lfc lfcse standard error
updated 8.5 years ago by • 0 • written 8.5 years ago by • 0
2
votes
1
reply
1.6k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 8.5 years ago by ★ 29k • written 8.5 years ago by ▴ 20
3
votes
1
reply
1.5k
views
RNASeq testing for differential expression in one condition, equality in another (using DESeq)
deseq2 deseq rnaseq
8.6 years ago ysdel ▴ 40
5
votes
3
replies
8.2k
views
What problem does the MA plot diagnose? And how do you solve it?
deseq2 deseq rnaseq
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by ▴ 40
2
votes
2
replies
3.3k
views
DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
deseq2 rlog variancestabilizingtransformation DESeq
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
0
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1
reply
2.2k
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DESeq pvalue & padj
DESeq
updated 8.6 years ago by ▴ 690 • written 8.6 years ago by • 0
0
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0
replies
1.6k
views
GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
8.6 years ago user31888 ▴ 30
1
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1
reply
2.1k
views
How to remove genes with 0 counts in tximport?
tximport deseq tximportdata deseq2
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 20
0
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0
replies
1.1k
views
DESeq: How are condition A and B assigned
deseq r
8.7 years ago arielle • 0
1
vote
2
replies
1.8k
views
DESeq2: linear combination trouble
paired samples deseq2 deseq
8.7 years ago JamesB • 0
0
votes
7
replies
6.2k
views
DESeq2 multiple factors nested design
DESeq DESeq2 DESeq DESeq2
updated 8.7 years ago by • 0 • written 11.5 years ago by ★ 13k
0
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1
reply
1.3k
views
how to change color of points log2foldchange>1
deseq
updated 8.8 years ago by ★ 13k • written 8.8 years ago by • 0
0
votes
7
replies
3.7k
views
Estimating group-specific dispersion in DESeq2
deseq2 deseq estimatedispersions
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
2
votes
6
replies
1.8k
views
DESeq2 multifactor test using batch as one of the factor
deseq2 deseq
updated 9.0 years ago by 43k • written 9.0 years ago by • 0
3
votes
8
replies
5.3k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing DESeq Sequencing DESeq
updated 9.1 years ago by • 0 • written 11.8 years ago by ★ 13k
2
votes
7
replies
1.8k
views
Factoring analysis and better design
deseq2 deseq
9.1 years ago arabella23 • 0
3
votes
5
replies
5.7k
views
Labeling points with hgnc symbols on the MA plot in DESeq2
deseq MA
updated 9.1 years ago by ▴ 150 • written 9.2 years ago by • 0
0
votes
3
replies
1.4k
views
DESeq outlier detection for unbalanced groups
deseq2 deseq outliers
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 30
2
votes
4
replies
4.7k
views
DESeq results names when using interaction terms
DESeq deseq2 resultsnames
9.2 years ago akaever ▴ 30
0
votes
7
replies
3.9k
views
Repeated Measures mRNA expression analysis II
limma edgeR DESeq
updated 9.2 years ago by • 0 • written 12.2 years ago by ▴ 140
0
votes
3
replies
1.2k
views
DESeq2 with paired data
deseq
9.3 years ago l.weissenburgermoser • 0
0
votes
2
replies
3.5k
views
Use surrogate variables on DESeq2
deseq2 sva deseq differential gene expression
updated 9.3 years ago by ▴ 20 • written 10.1 years ago by ▴ 40
1
vote
5
replies
5.6k
views
Heatmaps with replicates or triplicate data sets with counts to EdgeR, DESeq, or DESeq2
heatmap.2 heatmap edgeR deseq2 deseq
updated 9.4 years ago by 43k • written 9.4 years ago by ▴ 10
6
votes
12
replies
20k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 9.4 years ago by 43k • written 9.4 years ago by ▴ 10
3
votes
3
replies
2.3k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 9.4 years ago by ★ 13k • written 9.4 years ago by • 0
2
votes
4
replies
1.4k
views
Difference in differentially expressed genes captured from two sets of same sample
deseq2 deseq
updated 9.4 years ago by 43k • written 9.4 years ago by • 0
9
votes
6
replies
13k
views
Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 3.9 years ago by 43k • written 9.4 years ago by ▴ 10
1
vote
4
replies
11k
views
Difference between DESeq and DESeq2
Deseq deseq2 nbionormtest
updated 9.5 years ago by ★ 3.8k • written 9.5 years ago by ▴ 120
3
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4
replies
3.4k
views
DESeq is better than DESeq2?
deseq2 deseq
9.5 years ago ribioinfo ▴ 100
0
votes
2
replies
5.3k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
0
votes
4
replies
1.1k
views
DESeq2 experimental design
deseq
9.5 years ago Shucong Li ▴ 60
1
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2
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3.4k
views
DESeq - Change PCA axis from PasillaGuide to PC3 and PC4
deseq pca pasilla
updated 9.5 years ago by ▴ 180 • written 9.5 years ago by • 0
0
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4
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5.5k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
2
votes
2
replies
2.4k
views
Problem when installing DESeq on MAC OS X
s4vectors mac os x deseq
updated 9.6 years ago by ★ 13k • written 9.6 years ago by • 0
0
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1
reply
1.4k
views
code in supplementary 2 of DESeq
deseq
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 250
10
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14
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15k
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how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 4.5 years ago by ▴ 20 • written 9.6 years ago by ▴ 30
13
votes
6
replies
7.8k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 290
1
vote
1
reply
4.7k
views
Statistical power of limma vs mixed model approach to analyze microarray and differential proteomics/peptidomics experiments and Poisson/binomial mix…
RNASeq Microarray GO limma edgeR DESeq RNASeq Microarray GO limma edgeR DESeq
updated 9.8 years ago by 53k • written 12.2 years ago by ▴ 60
2
votes
3
replies
1.7k
views
allele specific expression in edgeR/DESeq
edger deseq2 deseq
updated 9.8 years ago by ★ 29k • written 9.8 years ago by ▴ 30
0
votes
10
replies
2.5k
views
What is the effect of setting modelMatrixType="standard"
deseq2 modelMatrixType DESeq
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 50
2
votes
10
replies
5.9k
views
DESEQ2 with 3 biological replicates for control and 1 biological replicate for treatment
DESEQ deseq2 deseq replicates biologicalreplicates
9.8 years ago wd ▴ 30
0
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1
reply
4.1k
views
DESeq2: too many NA for pvalues?
deseq2 deseq
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 120
6
votes
7
replies
4.7k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq deseq
9.8 years ago tonja.r ▴ 80
16
votes
5
replies
8.4k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 120
25
votes
11
replies
9.0k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 9.8 years ago by ★ 3.8k • written 9.8 years ago by ▴ 90
1
vote
2
replies
5.5k
views
DESeq2 - couldn't find the function called DESeqDataSetFromMatrix
deseq
updated 9.9 years ago by ★ 13k • written 9.9 years ago by • 0
1
vote
1
reply
1.9k
views
DESeq library installation
deseq
updated 9.9 years ago by 43k • written 9.9 years ago by • 0
7
votes
18
replies
10.0k
views
Differential expression analysis: Continuous variables
DESeq EdgeR limma
10.0 years ago Radek ▴ 90
512 results • Page 3 of 11
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Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexecutor4 • 0
FFH4X is a [Free Fire mod][1] menu APK that offers cheats like auto headshot, aimbot, ESP, wallhack, and unlimited skins. Players use it to…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
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Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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