Showing : timecourse • reset
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11
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
9 weeks ago • updated 8 weeks ago Denise • 0
0
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8
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553
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
11 weeks ago • updated 10 weeks ago Jiahao Tian • 0
0
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1
reply
727
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
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1
reply
500
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 11 months ago by 43k • written 11 months ago by • 0
2
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4
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842
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
12 months ago jihoon.kim.1495 ▴ 10
1
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3
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1.0k
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 17 months ago by 53k • written 17 months ago by • 0
0
votes
2
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966
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
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1
reply
723
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 21 months ago by 43k • written 21 months ago by • 0
0
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1
reply
751
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
21 months ago WS • 0
1
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6
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3.6k
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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 8.9 years ago by ▴ 10
1
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6
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3.3k
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Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
2
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1
reply
1.3k
views
DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 16 months ago by 43k • written 2.3 years ago by • 0
4
votes
5
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3.8k
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DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
1
reply
1.0k
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
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1
reply
994
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 2.9 years ago by 43k • written 3.0 years ago by • 0
3
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2
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1.5k
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time-series analysis using EdgeR
timecourse edgeR
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
0
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2
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3.5k
views
Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 3.4 years ago by ▴ 100 • written 3.4 years ago by • 0
0
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1
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1.1k
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DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 110
0
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1
reply
982
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Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 30
0
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3
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1.5k
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
5
votes
9
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2.3k
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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 4.2 years ago by 68k • written 4.2 years ago by ▴ 840
0
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2
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1.0k
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extracting within time-point differences from time-series model
DESeq2 TimeCourse
4.5 years ago serpalma.v ▴ 60
0
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2
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1.3k
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time couse RNAseq experiment 2 treatments x 4 times
edgeR timecourse
4.6 years ago Lina ▴ 10
0
votes
2
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1.2k
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 4.6 years ago by 53k • written 4.6 years ago by ▴ 10
1
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1
reply
3.7k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 4.8 years ago by 43k • written 4.8 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 13 months ago by 43k • written 10.6 years ago by ▴ 130
1
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1
reply
1.2k
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DESeq2 timecourse experiments
deseq2 timecourse
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
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3
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1.2k
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RNA seq time course design using DESeq2
deseq2 timecourse
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
votes
2
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1.3k
views
maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
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3
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1.3k
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Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
0
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3
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1.5k
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DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
6.1 years ago cp1015 • 0
4
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18
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27k
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DEseq2 time-series design.
deseq2 timecourse design
updated 6.3 years ago by • 0 • written 11.0 years ago by ▴ 100
0
votes
3
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1.6k
views
Is it possible to use DESeq2 likelihood ratio test for time-course analysis to analyse MNase-Seq data?
timecourse mnase-seq deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
vote
5
replies
2.1k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
4
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1.7k
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RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
7.1 years ago Maithê Barros ▴ 10
1
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1
reply
1.6k
views
Time Series Analysis
timecourse deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 20
0
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0
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1.1k
views
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
7.2 years ago rubi ▴ 110
0
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3
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1.4k
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time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 7.2 years ago by ★ 29k • written 7.2 years ago by • 0
1
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4
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1.8k
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Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
2
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3
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2.1k
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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 7.3 years ago by 43k • written 7.3 years ago by • 0
2
votes
2
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1.6k
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another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
1
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4
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2.8k
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How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 7.7 years ago by 53k • written 7.7 years ago by • 0
2
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4
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1.8k
views
Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 7.7 years ago by • 0 • written 7.7 years ago by • 0
0
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0
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1.4k
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Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
7.9 years ago jelisaveta.jeki.djordjevic • 0
0
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8
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2.3k
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edgeR: multi-subject time series analysis
timecourse multiple groups edgeR
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 80
0
votes
3
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1.5k
views
How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2 timecourse
updated 7.9 years ago by ★ 13k • written 7.9 years ago by • 0
4
votes
7
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3.4k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 7.9 years ago by 43k • written 8.8 years ago by ▴ 10
0
votes
8
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2.2k
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Time course experiments
deseq2 timecourse
8.0 years ago uu2110 • 0
2
votes
3
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2.5k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 3.3 years ago by • 0 • written 8.0 years ago by • 0
6
votes
19
replies
5.1k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 8.1 years ago by ▴ 690 • written 8.1 years ago by ▴ 50
121 results • Page 1 of 3
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry by teamardigen • 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
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Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
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Answer: DESeq2 design for haplotype MPRA
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