Showing : timecourse • reset
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
6
votes
19
replies
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
18
replies
24k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.8 years ago by • 0 • written 9.5 years ago by ▴ 100
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
0
votes
10
replies
2.0k
views
advice on limma design when analyzing for final outcome in timecourse data
limma timecourse
updated 9.5 years ago by ▴ 20 • written 9.5 years ago by ▴ 220
0
votes
10
replies
1.6k
views
Timecourse package
Microarray TimeCourse timecourse Microarray TimeCourse timecourse
updated 15.2 years ago by ▴ 440 • written 15.2 years ago by ▴ 380
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
5
votes
9
replies
1.5k
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 2.7 years ago by ▴ 830
0
votes
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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8
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1.6k
views
Time course experiments
deseq2 timecourse
6.5 years ago uu2110 • 0
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
9
votes
7
replies
9.2k
views
DESeq2 timecourse - How to set the experimental design
deseq2 geneexpression timecourse
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 10
0
votes
7
replies
1.6k
views
data preparation for timecourse
timecourse
updated 9.4 years ago by ★ 1.5k • written 9.4 years ago by • 0
0
votes
7
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2.7k
views
DESEQ ANODEV : A time course study
TimeCourse timecourse DESeq edgeR
updated 9.4 years ago by 50k • written 10.9 years ago by ▴ 20
3
votes
7
replies
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
4
votes
7
replies
2.6k
views
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
1
vote
6
replies
2.6k
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 7.4 years ago by ▴ 10
1
vote
6
replies
1.4k
views
edgeR time series DMSO correction
edger makecontrasts timecourse
updated 7.5 years ago by ★ 7.9k • written 7.5 years ago by ▴ 90
4
votes
6
replies
2.6k
views
Timecourse Differential expression with multiple factors
deseq2 edger timecourse
7.1 years ago anna_stavrinides ▴ 20
1
vote
6
replies
875
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
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
0
votes
5
replies
3.3k
views
coefficients meaning in time course analysis with DESeq2
deseq2 timecourse time course design and contrast matrix coefficient of variation
updated 8.5 years ago by 41k • written 8.5 years ago by ★ 1.5k
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
1
vote
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
7
votes
5
replies
1.6k
views
Which is the best design matrix to compare a timecourse between two conditions?
limma voom design matrix timecourse
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 10
6
votes
5
replies
2.1k
views
Limma : design and contrast for a timecourse experiment with 2 cell lines
limma limma design matrix timecourse
8.3 years ago Pierre-François Roux • 0
3
votes
5
replies
1.3k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
2
votes
4
replies
4.4k
views
LIMMA on matched time series data
timecourse limma
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 40
1
vote
4
replies
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
3
votes
4
replies
2.7k
views
Bioconductor vignette on Time course experiments only describes how to plot the the gene with the smallest p-value. How can I plot specific genes of …
timecourse time course rna-seq deseq2 ggplot2
8.6 years ago moldach ▴ 20
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
1
vote
4
replies
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
1
vote
4
replies
2.2k
views
DEXSeq continous variable in model
RNASeq TimeCourse timecourse DEXSeq DESeq2 RNASeq TimeCourse timecourse DEXSeq DESeq2
updated 9.7 years ago by ★ 1.9k • written 9.7 years ago by ▴ 650
0
votes
4
replies
1.5k
views
using timecourse package with non-replicated time course
Microarray TimeCourse timecourse Microarray TimeCourse timecourse
updated 12.8 years ago by ▴ 440 • written 12.8 years ago by ▴ 30
2
votes
4
replies
1.2k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
5.6 years ago Maithê Barros ▴ 10
2
votes
3
replies
1.7k
views
Deseq2 time series question,
rnaseq deseq2 timecourse
updated 7.5 years ago by 41k • written 7.5 years ago by • 0
1
vote
3
replies
2.9k
views
DESeq2 analysis for RNAseq data at different time points and different conditions
deseq2 timecourse rnaseq
updated 12 months ago by • 0 • written 7.4 years ago by ▴ 30
0
votes
3
replies
2.6k
views
Inherits(x,"data.frame") error in SamR
Microarray Normalization Preprocessing Bayesian Clustering TimeCourse Cancer affy vsn LPE
18.2 years ago McGee, Monnie ▴ 300
0
votes
3
replies
944
views
DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
4.6 years ago cp1015 • 0
0
votes
3
replies
1.7k
views
Timeseries loop design analysis using Limma or Maanova?
Bayesian Clustering TimeCourse timecourse oligo Bayesian Clustering TimeCourse timecourse
18.2 years ago Pete ▴ 70
0
votes
3
replies
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
votes
3
replies
819
views
RNA seq time course design using DESeq2
deseq2 timecourse
updated 3.6 years ago by 41k • written 3.6 years ago by • 0
2
votes
3
replies
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
0
votes
3
replies
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
2
votes
3
replies
844
views
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
3
votes
3
replies
1.9k
views
DESeq2 time series: error while measuring gene dispersion.
deseq2 timecourse
updated 9.2 years ago by 41k • written 9.2 years ago by ▴ 40
2
votes
3
replies
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
0
votes
3
replies
1.4k
views
[TimeCourse Package] Warnings message
Genetics TimeCourse timecourse Genetics TimeCourse timecourse
updated 18.3 years ago by ▴ 440 • written 18.3 years ago by ▴ 770
0
votes
3
replies
973
views
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
0
votes
3
replies
1.4k
views
timecourse + factorial + replicates in LIMMA
TimeCourse timecourse TimeCourse timecourse
updated 16.6 years ago by ★ 6.0k • written 16.6 years ago by ▴ 70
50 results • Page 1 of 1
Recent ...
Replies
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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