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 13 days ago by 65k • written 13 days ago by • 0
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1
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229
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 12 weeks ago by 41k • written 3 months ago by • 0
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1
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249
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
1
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6
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2.6k
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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 7.4 years ago by ▴ 10
1
vote
6
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864
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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
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481
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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
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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
546
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 10 months ago by 41k • written 10 months ago by • 0
0
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1
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602
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 16 months ago by 41k • written 17 months ago by • 0
3
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2
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953
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time-series analysis using EdgeR
timecourse edgeR
updated 22 months ago by 50k • written 22 months ago by • 0
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2
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1.8k
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Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 22 months ago by ▴ 90 • written 23 months ago by • 0
0
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1
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694
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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
0
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1
reply
683
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by ▴ 30
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3
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977
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
5
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9
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1.5k
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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 2.7 years ago by 65k • written 2.7 years ago by ▴ 830
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2
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695
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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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948
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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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871
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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 3.2 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
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1
reply
802
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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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815
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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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819
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maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
2
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3
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840
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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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938
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DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
4.5 years ago cp1015 • 0
4
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18
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24k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.8 years ago by • 0 • written 9.5 years ago by ▴ 100
0
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3
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1.1k
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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 41k • written 5.1 years ago by • 0
1
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5
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1.4k
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Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 5.3 years ago by 41k • written 5.3 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
5.6 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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847
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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969
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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
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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 5.8 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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2.1k
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
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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 6.2 years ago by • 0 • written 6.2 years ago by • 0
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
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 6.4 years ago by ★ 28k • written 6.4 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 6.4 years ago by ★ 13k • written 6.4 years ago by • 0
4
votes
7
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2.6k
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GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.4 years ago by 41k • written 7.3 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
6.5 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 22 months ago by • 0 • written 6.5 years ago by • 0
6
votes
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
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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
6.7 years ago heikki.sarin ▴ 10
3
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7
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2.9k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 6.7 years ago by ▴ 680 • written 6.7 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
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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 2.9 years ago by • 0 • written 6.8 years ago by ▴ 20
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Answer: Log-cpm values from limma by Gordon Smyth 50k
The log-cpm values from voom() are not free of batch effect. If you want batch-corrected log-cpm values, we recommend cpm() followed by rem…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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