Showing : timecourse • reset
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4
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348
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
3 months ago • updated 12 weeks ago Denise • 0
0
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11
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832
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
6 months ago • updated 5 months ago Denise • 0
0
votes
8
replies
740
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
0
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1
reply
834
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
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1
reply
586
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 15 months ago by 43k • written 15 months ago by • 0
2
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4
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1.1k
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
16 months ago jihoon.kim.1495 ▴ 10
1
vote
3
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1.2k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 21 months ago by 53k • written 21 months ago by • 0
0
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2
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1.2k
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 22 months ago by 68k • written 22 months ago by • 0
0
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1
reply
844
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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1
reply
900
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
2.1 years ago WS • 0
1
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6
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3.9k
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 9.2 years ago by ▴ 10
1
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6
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4.0k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
votes
1
reply
1.4k
views
DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 19 months ago by 43k • written 2.6 years ago by • 0
4
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5
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4.3k
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DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
0
votes
1
reply
1.2k
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
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1
reply
1.2k
views
Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 3.2 years ago by 43k • written 3.3 years ago by • 0
3
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2
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1.6k
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time-series analysis using EdgeR
timecourse edgeR
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
0
votes
2
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3.8k
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Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 3.7 years ago by ▴ 100 • written 3.7 years ago by • 0
0
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1
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1.2k
views
DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 110
0
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1
reply
1.1k
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Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 20
0
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3
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1.6k
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
5
votes
9
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2.5k
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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 4.6 years ago by 68k • written 4.6 years ago by ▴ 840
0
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2
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1.1k
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extracting within time-point differences from time-series model
DESeq2 TimeCourse
4.8 years ago serpalma.v ▴ 60
0
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2
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1.4k
views
time couse RNAseq experiment 2 treatments x 4 times
edgeR timecourse
4.9 years ago Lina ▴ 10
0
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2
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1.4k
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 10
1
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1
reply
4.1k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
34
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29
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17k
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[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 17 months ago by 43k • written 10.9 years ago by ▴ 130
1
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1
reply
1.3k
views
DESeq2 timecourse experiments
deseq2 timecourse
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
3
replies
1.3k
views
RNA seq time course design using DESeq2
deseq2 timecourse
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
2
replies
1.5k
views
maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
2
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3
replies
1.4k
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Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 5.9 years ago by ★ 4.0k • written 5.9 years ago by • 0
0
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3
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1.6k
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DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
6.4 years ago cp1015 • 0
4
votes
18
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28k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 6.6 years ago by • 0 • written 11.3 years ago by ▴ 100
0
votes
3
replies
1.7k
views
Is it possible to use DESeq2 likelihood ratio test for time-course analysis to analyse MNase-Seq data?
timecourse mnase-seq deseq2
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
1
vote
5
replies
2.3k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
2
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4
replies
1.9k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
7.4 years ago Maithê Barros ▴ 10
1
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1
reply
1.7k
views
Time Series Analysis
timecourse deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 20
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0
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1.2k
views
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
7.5 years ago rubi ▴ 110
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3
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1.5k
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time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 7.5 years ago by ★ 29k • written 7.5 years ago by • 0
1
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4
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2.0k
views
Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
2
votes
3
replies
2.2k
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 7.6 years ago by 43k • written 7.6 years ago by • 0
2
votes
2
replies
1.7k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 7.7 years ago by 53k • written 7.7 years ago by • 0
1
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4
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2.9k
views
How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 8.0 years ago by 53k • written 8.0 years ago by • 0
2
votes
4
replies
1.9k
views
Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 8.0 years ago by • 0 • written 8.0 years ago by • 0
0
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0
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1.5k
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Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
8.2 years ago jelisaveta.jeki.djordjevic • 0
0
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8
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2.5k
views
edgeR: multi-subject time series analysis
timecourse multiple groups edgeR
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 80
0
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3
replies
1.7k
views
How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2 timecourse
updated 8.2 years ago by ★ 13k • written 8.2 years ago by • 0
4
votes
7
replies
3.6k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 8.3 years ago by 43k • written 9.1 years ago by ▴ 10
0
votes
8
replies
2.3k
views
Time course experiments
deseq2 timecourse
8.3 years ago uu2110 • 0
2
votes
3
replies
2.6k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 3.7 years ago by • 0 • written 8.3 years ago by • 0
122 results • Page 1 of 3
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Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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