Showing : TimeCourse • reset
1
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 5 days ago by 50k • written 6 days ago by • 0
0
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2
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183
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
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1
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256
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 4 months ago by 42k • written 4 months ago by • 0
0
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1
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290
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
1
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6
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2.7k
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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
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973
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Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
0
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1
reply
532
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DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
3
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5
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1.4k
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DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
0
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1
reply
576
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 11 months ago by 42k • written 11 months ago by • 0
0
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1
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627
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 17 months ago by 42k • written 18 months ago by • 0
3
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time-series analysis using EdgeR
timecourse edgeR
updated 23 months ago by 50k • written 23 months ago by • 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 24 months ago by • 0
0
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1
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723
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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 42k • written 2.2 years ago by ▴ 90
0
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1
reply
707
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Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 2.6 years ago by 42k • written 2.6 years ago by ▴ 30
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3
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
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9
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1.6k
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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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719
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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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971
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time couse RNAseq experiment 2 treatments x 4 times
edgeR timecourse
3.2 years ago HS ▴ 10
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2
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890
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edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 10
1
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1
reply
2.5k
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DESeq2 time course analysis
DESeq2 Timecourse
updated 3.3 years ago by 42k • 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 3.3 years ago by • 0 • written 9.2 years ago by ▴ 120
1
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1
reply
823
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DESeq2 timecourse experiments
deseq2 timecourse
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
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3
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834
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RNA seq time course design using DESeq2
deseq2 timecourse
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
0
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2
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851
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maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 3.9 years ago by 42k • written 3.9 years ago by • 0
2
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3
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865
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Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by • 0
0
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3
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967
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DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
4.6 years ago cp1015 • 0
4
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18
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24k
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DEseq2 time-series design.
deseq2 timecourse design
updated 4.9 years ago by • 0 • written 9.5 years ago by ▴ 100
0
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3
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1.2k
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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 42k • written 5.2 years ago by • 0
1
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5
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1.5k
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Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
2
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4
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1.2k
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RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
5.7 years ago Maithê Barros ▴ 10
1
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1
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1.2k
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Time Series Analysis
timecourse deseq2
updated 5.8 years ago by 42k • written 5.8 years ago by ▴ 20
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0
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868
views
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
5.8 years ago rubi ▴ 110
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3
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999
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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
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Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 5.9 years ago by 42k • written 5.9 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 42k • written 5.9 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 6.0 years ago by 50k • written 6.0 years ago by • 0
1
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4
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2.2k
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How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 6.3 years ago by 50k • written 6.3 years ago by • 0
2
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4
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1.3k
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Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 6.3 years ago by • 0 • written 6.3 years ago by • 0
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0
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1.1k
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Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
6.4 years ago jelisaveta.jeki.djordjevic • 0
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8
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1.6k
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edgeR: multi-subject time series analysis
timecourse multiple groups edgeR
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 80
0
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3
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1.1k
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How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2 timecourse
updated 6.5 years ago by ★ 13k • written 6.5 years ago by • 0
4
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7
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2.7k
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GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.5 years ago by 42k • written 7.4 years ago by ▴ 10
0
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8
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1.6k
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Time course experiments
deseq2 timecourse
6.6 years ago uu2110 • 0
2
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3
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1.9k
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What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 23 months ago by • 0 • written 6.6 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
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8
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2.2k
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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
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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 6.9 years ago by 42k • written 6.9 years ago by • 0
2
votes
5
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1.8k
views
DESeq2 time series tissue specific differences over time
deseq2 timecourse multiple time points rnaseq
6.9 years ago Nicholas Owen • 0
50 results • Page 1 of 1
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Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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