Showing : timecourse • reset
1
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3
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501
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 3 months ago by 51k • written 3 months ago by • 0
0
votes
2
replies
336
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
0
votes
1
reply
391
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 7 months ago by 42k • written 7 months ago by • 0
0
votes
1
reply
442
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
8 months ago WS • 0
1
vote
6
replies
3.0k
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 7.8 years ago by ▴ 10
1
vote
6
replies
1.6k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 12 months ago by ★ 4.4k • written 12 months ago by • 0
2
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1
reply
739
views
DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 10 weeks ago by 42k • written 14 months ago by • 0
4
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5
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2.0k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 13 months ago by 42k • written 14 months ago by • 0
0
votes
1
reply
681
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 15 months ago by 42k • written 15 months ago by • 0
0
votes
1
reply
734
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 21 months ago by 42k • written 22 months ago by • 0
3
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2
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1.1k
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time-series analysis using EdgeR
timecourse edgeR
updated 2.3 years ago by 51k • written 2.3 years ago by • 0
0
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2
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2.2k
views
Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 2.3 years ago by ▴ 90 • written 2.3 years ago by • 0
0
votes
1
reply
826
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DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 2.5 years ago by 42k • written 2.5 years ago by ▴ 110
0
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1
reply
772
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 2.9 years ago by 42k • written 2.9 years ago by ▴ 30
0
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3
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1.2k
views
DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
5
votes
9
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1.8k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 3.1 years ago by 67k • written 3.1 years ago by ▴ 830
0
votes
2
replies
790
views
extracting within time-point differences from time-series model
DESeq2 TimeCourse
3.4 years ago serpalma.v ▴ 60
0
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2
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1.1k
views
time couse RNAseq experiment 2 treatments x 4 times
edgeR timecourse
3.5 years ago HS ▴ 10
0
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2
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979
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 3.5 years ago by 51k • written 3.5 years ago by ▴ 10
1
vote
1
reply
2.8k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
18
votes
24
replies
14k
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[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 3.6 years ago by • 0 • written 9.5 years ago by ▴ 120
1
vote
1
reply
917
views
DESeq2 timecourse experiments
deseq2 timecourse
updated 4.0 years ago by 42k • written 4.0 years ago by • 0
0
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3
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931
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RNA seq time course design using DESeq2
deseq2 timecourse
updated 4.0 years ago by 42k • written 4.0 years ago by • 0
0
votes
2
replies
965
views
maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
2
votes
3
replies
973
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
0
votes
3
replies
1.1k
views
DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
4.9 years ago cp1015 • 0
4
votes
18
replies
25k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 5.2 years ago by • 0 • written 9.8 years ago by ▴ 100
0
votes
3
replies
1.3k
views
Is it possible to use DESeq2 likelihood ratio test for time-course analysis to analyse MNase-Seq data?
timecourse mnase-seq deseq2
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
1
vote
5
replies
1.6k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
2
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4
replies
1.3k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
6.0 years ago Maithê Barros ▴ 10
1
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1
reply
1.4k
views
Time Series Analysis
timecourse deseq2
updated 6.1 years ago by 42k • written 6.1 years ago by ▴ 20
0
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0
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946
views
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
6.1 years ago rubi ▴ 110
0
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3
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1.1k
views
time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
1
vote
4
replies
1.4k
views
Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 6.2 years ago by 42k • written 6.2 years ago by • 0
2
votes
3
replies
1.6k
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 6.2 years ago by 42k • written 6.2 years ago by • 0
2
votes
2
replies
1.3k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 6.3 years ago by 51k • written 6.3 years ago by • 0
1
vote
4
replies
2.3k
views
How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 6.6 years ago by 51k • written 6.6 years ago by • 0
2
votes
4
replies
1.4k
views
Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 6.6 years ago by • 0 • written 6.6 years ago by • 0
0
votes
0
replies
1.2k
views
Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
6.7 years ago jelisaveta.jeki.djordjevic • 0
0
votes
8
replies
1.7k
views
edgeR: multi-subject time series analysis
timecourse multiple groups edgeR
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 80
0
votes
3
replies
1.2k
views
How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2 timecourse
updated 6.8 years ago by ★ 13k • written 6.8 years ago by • 0
4
votes
7
replies
2.8k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.8 years ago by 42k • written 7.7 years ago by ▴ 10
0
votes
8
replies
1.7k
views
Time course experiments
deseq2 timecourse
6.9 years ago uu2110 • 0
2
votes
3
replies
2.0k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 2.2 years ago by • 0 • written 6.9 years ago by • 0
6
votes
19
replies
3.9k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 7.0 years ago by ▴ 690 • written 7.0 years ago by ▴ 50
4
votes
8
replies
2.3k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR edger "glmqlftest()" timecourse model
updated 7.1 years ago by ★ 7.9k • written 7.1 years ago by ▴ 10
0
votes
0
replies
1.3k
views
How construct a model for case-control time-course experiment in DEXseq?
dexseq timecourse model.matrix model
7.1 years ago heikki.sarin ▴ 10
3
votes
7
replies
3.1k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 7.1 years ago by ▴ 690 • written 7.1 years ago by • 0
2
votes
1
reply
1.1k
views
DEseq2 time-series before and after Infection
multiple factor design deseq2 timecourse
updated 7.2 years ago by 42k • written 7.2 years ago by • 0
2
votes
5
replies
2.0k
views
DESeq2 time series tissue specific differences over time
deseq2 timecourse multiple time points rnaseq
7.2 years ago Nicholas Owen • 0
50 results • Page 1 of 1
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Comment: SingleR Label.Ont by Stepah • 0
[Aussie Play][1] cares about its Australian players by offering a safe and secure gaming experience where there is never a dull moment. The…
Comment: ensemblVEP deprecation and how to reproduce by Vincent J. Carey, Jr. 6.7k
What aspect of ensemblVEP are you looking for? The vignette https://bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/in…
Answer: Help with design matrix for RNA-seq data using edgeR by Gordon Smyth 51k
This forum is intended to help with software usage and syntax rather than to answer research questions, and your question is a definitely a…
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by Michael Love 42k
DESeq2 has a way of fixing the reference pseudo-sample used for normalization. In estimateSizeFactors man page, you will see an argument g…
Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by Michael Love 42k
Sorry - I requested this to be posted here, I will answer.
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Answer: Help with design matrix for RNA-seq data using edgeR
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