Showing : TimeCourse • reset
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 24 days ago by ★ 4.8k • written 25 days ago by • 0
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1
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363
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 5 months ago by 43k • written 5 months ago by • 0
2
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4
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615
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
6 months ago jihoon.kim.1495 ▴ 10
1
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3
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837
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 11 months ago by 52k • written 11 months ago by • 0
0
votes
2
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704
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 12 months ago by 68k • written 12 months ago by • 0
0
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1
reply
581
views
Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 15 months ago by 43k • written 15 months ago by • 0
0
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1
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632
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
15 months ago WS • 0
1
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6
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3.4k
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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 8.4 years ago by ▴ 10
1
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6
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2.8k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 20 months ago by ★ 4.8k • written 20 months ago by • 0
2
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1
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1.1k
views
DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 9 months ago by 43k • written 21 months ago by • 0
4
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5
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3.3k
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DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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1
reply
863
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 22 months ago by 43k • written 23 months ago by • 0
0
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1
reply
897
views
Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 2.4 years ago by 43k • written 2.5 years ago by • 0
3
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2
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1.3k
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time-series analysis using EdgeR
timecourse edgeR
updated 2.9 years ago by 52k • written 2.9 years ago by • 0
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2
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3.2k
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Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 2.9 years ago by ▴ 90 • written 2.9 years ago by • 0
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1
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996
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DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 110
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1
reply
895
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 30
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3
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1.3k
views
DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
5
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9
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2.1k
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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 3.7 years ago by 68k • written 3.7 years ago by ▴ 840
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2
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922
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extracting within time-point differences from time-series model
DESeq2 TimeCourse
4.0 years ago serpalma.v ▴ 60
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2
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1.2k
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time couse RNAseq experiment 2 treatments x 4 times
edgeR timecourse
4.1 years ago Lina ▴ 10
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2
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1.1k
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edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 4.1 years ago by 52k • written 4.1 years ago by ▴ 10
1
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1
reply
3.4k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
34
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29
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16k
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[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 7 months ago by 43k • written 10.1 years ago by ▴ 130
1
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1
reply
1.1k
views
DESeq2 timecourse experiments
deseq2 timecourse
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
0
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3
replies
1.1k
views
RNA seq time course design using DESeq2
deseq2 timecourse
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
0
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2
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1.2k
views
maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
2
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3
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1.1k
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Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
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3
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1.3k
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DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
5.6 years ago cp1015 • 0
4
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18
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26k
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DEseq2 time-series design.
deseq2 timecourse design
updated 5.8 years ago by • 0 • written 10.5 years ago by ▴ 100
0
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3
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1.4k
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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 6.1 years ago by 43k • written 6.1 years ago by • 0
1
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5
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1.9k
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Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
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4
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1.6k
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RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
6.6 years ago Maithê Barros ▴ 10
1
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1
reply
1.5k
views
Time Series Analysis
timecourse deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 20
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0
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1.0k
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Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
6.7 years ago rubi ▴ 110
0
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3
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1.3k
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time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
1
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4
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1.6k
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Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
2
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3
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1.9k
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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 6.8 years ago by 43k • written 6.8 years ago by • 0
2
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2
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1.5k
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another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 6.9 years ago by 52k • written 6.9 years ago by • 0
1
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4
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2.6k
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How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 7.2 years ago by 52k • written 7.2 years ago by • 0
2
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4
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1.7k
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Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 7.2 years ago by • 0 • written 7.2 years ago by • 0
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0
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1.3k
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Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
7.4 years ago jelisaveta.jeki.djordjevic • 0
0
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8
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2.0k
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edgeR: multi-subject time series analysis
timecourse multiple groups edgeR
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 80
0
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3
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1.4k
views
How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2 timecourse
updated 7.4 years ago by ★ 13k • written 7.4 years ago by • 0
4
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7
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3.2k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 7.4 years ago by 43k • written 8.3 years ago by ▴ 10
0
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8
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2.0k
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Time course experiments
deseq2 timecourse
7.5 years ago uu2110 • 0
2
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3
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2.3k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 2.8 years ago by • 0 • written 7.5 years ago by • 0
6
votes
19
replies
4.6k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 7.6 years ago by ▴ 690 • written 7.6 years ago by ▴ 50
4
votes
8
replies
2.6k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR edger "glmqlftest()" timecourse model
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 10
0
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0
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1.4k
views
How construct a model for case-control time-course experiment in DEXseq?
dexseq timecourse model.matrix model
7.7 years ago heikki.sarin ▴ 10
50 results • Page 1 of 1
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Replies
Comment: How to convert transcript counts to gene counts in R? by ben • 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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