Showing : timecourse • reset
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 29 days ago by 65k • written 29 days ago by • 0
0
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1
reply
242
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 3 months ago by 41k • written 3 months ago by • 0
0
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1
reply
269
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
1
vote
6
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2.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.5 years ago by ▴ 10
1
vote
6
replies
916
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
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1
reply
510
views
DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
3
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5
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1.3k
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DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 9 months ago by 41k • written 10 months ago by • 0
0
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1
reply
562
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 11 months ago by 41k • written 11 months ago by • 0
0
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1
reply
618
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 17 months ago by 41k • written 18 months ago by • 0
3
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2
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982
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time-series analysis using EdgeR
timecourse edgeR
updated 23 months ago by 50k • written 23 months ago by • 0
0
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2
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1.9k
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Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 23 months ago by ▴ 90 • written 23 months ago by • 0
0
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1
reply
708
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DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 2.2 years ago by 41k • written 2.2 years ago by ▴ 90
0
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1
reply
699
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 2.6 years ago by 41k • written 2.6 years ago by ▴ 30
0
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3
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995
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
5
votes
9
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1.6k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.8 years ago by 65k • written 2.8 years ago by ▴ 830
0
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2
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705
views
extracting within time-point differences from time-series model
DESeq2 TimeCourse
3.0 years ago serpalma.v ▴ 60
0
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2
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962
views
time couse RNAseq experiment 2 treatments x 4 times
edgeR timecourse
3.1 years ago HS ▴ 10
0
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2
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881
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 10
1
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1
reply
2.5k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 3.3 years ago by 41k • written 3.3 years ago by • 0
18
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24
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14k
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[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 3.2 years ago by • 0 • written 9.1 years ago by ▴ 120
1
vote
1
reply
813
views
DESeq2 timecourse experiments
deseq2 timecourse
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
0
votes
3
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826
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RNA seq time course design using DESeq2
deseq2 timecourse
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
0
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2
replies
833
views
maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 3.9 years ago by 41k • written 3.9 years ago by • 0
2
votes
3
replies
858
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
0
votes
3
replies
951
views
DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
4.6 years ago cp1015 • 0
4
votes
18
replies
24k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.8 years ago by • 0 • written 9.5 years ago by ▴ 100
0
votes
3
replies
1.2k
views
Is it possible to use DESeq2 likelihood ratio test for time-course analysis to analyse MNase-Seq data?
timecourse mnase-seq deseq2
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
1
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5
replies
1.4k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
2
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4
replies
1.2k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
5.6 years ago Maithê Barros ▴ 10
1
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1
reply
1.2k
views
Time Series Analysis
timecourse deseq2
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 20
0
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0
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861
views
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
5.7 years ago rubi ▴ 110
0
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3
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980
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time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
1
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4
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1.3k
views
Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
2
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3
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1.5k
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DESeq2 for time series using time as continuous and looking at effect of time on DE
deseq2 timecourse multiple time points mlr michael love
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
2
votes
2
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1.2k
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another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 5.9 years ago by 50k • written 5.9 years ago by • 0
1
vote
4
replies
2.2k
views
How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
2
votes
4
replies
1.3k
views
Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 6.2 years ago by • 0 • written 6.2 years ago by • 0
0
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0
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1.1k
views
Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
6.4 years ago jelisaveta.jeki.djordjevic • 0
0
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8
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1.6k
views
edgeR: multi-subject time series analysis
timecourse multiple groups edgeR
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 80
0
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3
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1.1k
views
How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2 timecourse
updated 6.4 years ago by ★ 13k • written 6.4 years ago by • 0
4
votes
7
replies
2.6k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.5 years ago by 41k • written 7.3 years ago by ▴ 10
0
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8
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1.6k
views
Time course experiments
deseq2 timecourse
6.5 years ago uu2110 • 0
2
votes
3
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1.9k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 22 months ago by • 0 • written 6.5 years ago by • 0
6
votes
19
replies
3.6k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by ▴ 50
4
votes
8
replies
2.2k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR edger "glmqlftest()" timecourse model
updated 6.8 years ago by ★ 7.9k • written 6.8 years ago by ▴ 10
0
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0
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1.2k
views
How construct a model for case-control time-course experiment in DEXseq?
dexseq timecourse model.matrix model
6.8 years ago heikki.sarin ▴ 10
3
votes
7
replies
2.9k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 6.8 years ago by ▴ 680 • written 6.8 years ago by • 0
2
votes
1
reply
1.0k
views
DEseq2 time-series before and after Infection
multiple factor design deseq2 timecourse
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
2
votes
5
replies
1.8k
views
DESeq2 time series tissue specific differences over time
deseq2 timecourse multiple time points rnaseq
6.8 years ago Nicholas Owen • 0
0
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2
replies
3.0k
views
Time-course analysis with limma for >3 time points
limma contrast matrix design matrix multiple time points timecourse
updated 3.0 years ago by • 0 • written 6.9 years ago by ▴ 20
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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