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 21 days ago by 65k • written 21 days ago by • 0
0
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1
reply
236
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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
256
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
1
vote
6
replies
893
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
0
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1
reply
494
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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
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
0
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1
reply
556
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 10 months ago by 41k • written 11 months ago by • 0
0
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1
reply
610
views
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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970
views
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
views
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
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702
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DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 90
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1
reply
689
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by ▴ 30
0
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3
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986
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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
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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 2.7 years ago by 65k • written 2.8 years ago by ▴ 830
0
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2
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701
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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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959
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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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878
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
vote
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
1
vote
1
reply
805
views
DESeq2 timecourse experiments
deseq2 timecourse
updated 3.6 years ago by 41k • written 3.6 years ago by • 0
0
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3
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823
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RNA seq time course design using DESeq2
deseq2 timecourse
updated 3.6 years ago by 41k • written 3.6 years ago by • 0
0
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2
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829
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
848
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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
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3
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945
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DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
4.6 years ago cp1015 • 0
0
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3
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1.1k
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
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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
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1.2k
views
Time Series Analysis
timecourse deseq2
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 20
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0
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854
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
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3
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975
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time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 5.7 years ago by ★ 28k • written 5.7 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
views
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 5.8 years ago by 41k • written 5.8 years ago by • 0
2
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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
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4
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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
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
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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
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19
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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
2.1k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR edger "glmqlftest()" timecourse model
updated 6.7 years ago by ★ 7.9k • written 6.7 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
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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
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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
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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 6.8 years ago by ▴ 20
7
votes
9
replies
7.0k
views
DESeq2 time series analysis
DESEQ2 timecourse multiple time points time
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 10
4
votes
6
replies
2.6k
views
Timecourse Differential expression with multiple factors
deseq2 edger timecourse
7.2 years ago • updated 7.1 years ago anna_stavrinides ▴ 20
4
votes
6
replies
1.5k
views
Multi-factorial design for patient-replicates from different time points (Deseq2)
deseq2 rnaseq timecourse multiple time points multifactorial design
updated 7.2 years ago by 41k • written 7.2 years ago by • 0
1
vote
11
replies
4.3k
views
Time-series Analysis using DESeq2 and LRT test
deseq2 LRT timecourse
updated 2.1 years ago by 41k • written 7.2 years ago by ★ 1.5k
50 results • Page 1 of 1
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Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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