Showing : TimeCourse • reset
1
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3
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 months ago by 51k • written 4 months ago by • 0
0
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2
replies
361
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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
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1
reply
409
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 8 months ago by 42k • written 8 months ago by • 0
0
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1
reply
458
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
8 months ago WS • 0
1
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6
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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 7.9 years ago by ▴ 10
1
vote
6
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1.7k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 13 months ago by ★ 4.4k • written 13 months ago by • 0
2
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1
reply
759
views
DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 3 months ago by 42k • written 14 months ago by • 0
4
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5
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2.1k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 14 months ago by 42k • written 14 months ago by • 0
0
votes
1
reply
700
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 16 months ago by 42k • written 16 months ago by • 0
0
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1
reply
747
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 22 months ago by 42k • written 23 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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2.3k
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
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1
reply
845
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DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 2.6 years ago by 42k • written 2.6 years ago by ▴ 110
0
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1
reply
781
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 3.0 years ago by 42k • written 3.0 years ago by ▴ 30
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3
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1.2k
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 3.1 years ago by 42k • written 3.1 years ago by • 0
5
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9
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1.8k
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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 3.2 years ago by 67k • written 3.2 years ago by ▴ 830
0
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2
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803
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
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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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993
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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
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1
reply
2.9k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
34
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29
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15k
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[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 16 days ago by 42k • written 9.5 years ago by ▴ 130
1
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1
reply
932
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DESeq2 timecourse experiments
deseq2 timecourse
updated 4.1 years ago by 42k • written 4.1 years ago by • 0
0
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3
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951
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RNA seq time course design using DESeq2
deseq2 timecourse
updated 4.1 years ago by 42k • written 4.1 years ago by • 0
0
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2
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982
views
maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 4.3 years ago by 42k • written 4.3 years ago by • 0
2
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3
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985
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
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3
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1.1k
views
DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
5.0 years ago cp1015 • 0
4
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18
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25k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 5.2 years ago by • 0 • written 9.9 years ago by ▴ 100
0
votes
3
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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
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5
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1.6k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 5.8 years ago by 42k • written 5.8 years ago by • 0
2
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4
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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
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1.4k
views
Time Series Analysis
timecourse deseq2
updated 6.1 years ago by 42k • written 6.1 years ago by ▴ 20
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0
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956
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 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
1
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4
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1.5k
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
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3
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1.7k
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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 6.3 years ago by 42k • written 6.3 years ago by • 0
2
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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
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4
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2.4k
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
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1.5k
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
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0
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1.2k
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Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
6.8 years ago jelisaveta.jeki.djordjevic • 0
0
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8
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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
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2.8k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.9 years ago by 42k • written 7.7 years ago by ▴ 10
0
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8
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1.7k
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Time course experiments
deseq2 timecourse
6.9 years ago uu2110 • 0
2
votes
3
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2.0k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 2.3 years ago by • 0 • written 6.9 years ago by • 0
6
votes
19
replies
4.0k
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
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2.4k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR edger "glmqlftest()" timecourse model
updated 7.2 years ago by ★ 7.9k • written 7.2 years ago by ▴ 10
0
votes
0
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1.3k
views
How construct a model for case-control time-course experiment in DEXseq?
dexseq timecourse model.matrix model
7.2 years ago heikki.sarin ▴ 10
3
votes
7
replies
3.2k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 7.2 years ago by ▴ 690 • written 7.2 years ago by • 0
2
votes
1
reply
1.2k
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: How should I run ssGSEA Hallmark Enrichment Analysis? by Ginny • 0
I think the other side of this question is that the non protein coding genes would be in the "background", they would influence the ranking…
Comment: ISO a solution to rank-order introns by transcript by James W. MacDonald 67k
There's an error in the last line. Note that `sapply(lengths(z), seq_len)` will return a `list` because the lengths vary. We need a vector,…
Comment: BiomaRt - improved access to Ensembl ? by Mike Smith ★ 6.5k
Why do you want to use `useMart()` rather than `useEnsembl()`? They are essentially the same (`useEnsembl()` will eventually call `useMart(…
Comment: Installing Bioconductor packages in Docker by devarti.mahakalkar • 0
I have installed BiocManager on my base image rather than having it as base image. RUN Rscript -e "install.packages('BiocManager', re…
Comment: Meta-analysis on RNA-seq data sets by Travis • 0
Thank you for your suggestions and explanation of your approach!
Votes
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: addPatternDensity in 'qsea' takes too much time
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