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 19 days ago by 65k • written 19 days ago by • 0
0
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2
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1.4k
views
DE genes over time with DESeq2
deseq2 timecourse design and contrast matrix
updated 6 weeks ago by ▴ 10 • written 8.5 years ago by ★ 1.5k
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1
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236
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 3 months ago by 41k • written 3 months ago by • 0
0
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1
reply
255
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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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890
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
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
486
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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
0
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1
reply
553
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 10 months ago by 41k • written 11 months ago by • 0
1
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3
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2.9k
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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
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1
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608
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 17 months ago by 41k • written 17 months ago by • 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
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 23 months ago by • 0
3
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2
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967
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time-series analysis using EdgeR
timecourse edgeR
updated 23 months ago by 50k • written 23 months ago by • 0
1
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11
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4.3k
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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
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1
reply
702
views
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
687
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Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by ▴ 30
0
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3
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984
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 2.6 years ago by 41k • written 2.7 years ago by • 0
5
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9
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1.6k
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
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2
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3.0k
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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
0
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2
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701
views
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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957
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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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877
views
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
18
votes
24
replies
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
vote
1
reply
2.5k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 3.3 years ago by 41k • written 3.3 years ago by • 0
1
vote
1
reply
805
views
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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821
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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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827
views
maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 3.9 years ago by 41k • written 3.9 years ago by • 0
2
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3
replies
845
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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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944
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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 4.8 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 5.4 years ago by 41k • 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
5.6 years ago Maithê Barros ▴ 10
1
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1
reply
1.2k
views
Time Series Analysis
timecourse deseq2
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 20
0
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0
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853
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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
0
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3
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974
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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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2.2k
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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
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
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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
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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
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
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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
50 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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