Showing : timecourse • reset
0
votes
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224
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
2
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4
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431
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
10 weeks ago jihoon.kim.1495 ▴ 10
1
vote
3
replies
656
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 7 months ago by 52k • written 7 months ago by • 0
0
votes
2
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476
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 8 months ago by 67k • written 8 months ago by • 0
0
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1
reply
472
views
Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 11 months ago by 43k • written 11 months ago by • 0
0
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1
reply
536
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
11 months ago WS • 0
1
vote
6
replies
3.1k
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 8.1 years ago by ▴ 10
1
vote
6
replies
2.1k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
2
votes
1
reply
901
views
DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 5 months ago by 43k • written 17 months ago by • 0
4
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5
replies
2.5k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
0
votes
1
reply
758
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 18 months ago by 43k • written 19 months ago by • 0
0
votes
1
reply
806
views
Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
3
votes
2
replies
1.2k
views
time-series analysis using EdgeR
timecourse edgeR
updated 2.6 years ago by 52k • written 2.6 years ago by • 0
0
votes
2
replies
2.6k
views
Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 2.6 years ago by ▴ 90 • written 2.6 years ago by • 0
0
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1
reply
916
views
DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 110
0
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1
reply
824
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 30
0
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3
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1.2k
views
DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
5
votes
9
replies
1.9k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 3.4 years ago by 67k • written 3.4 years ago by ▴ 840
0
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2
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850
views
extracting within time-point differences from time-series model
DESeq2 TimeCourse
3.6 years ago serpalma.v ▴ 60
0
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2
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1.2k
views
time couse RNAseq experiment 2 treatments x 4 times
edgeR timecourse
3.8 years ago Lina ▴ 10
0
votes
2
replies
1.0k
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 3.8 years ago by 52k • written 3.8 years ago by ▴ 10
1
vote
1
reply
3.1k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
34
votes
29
replies
15k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 3 months ago by 43k • written 9.8 years ago by ▴ 130
1
vote
1
reply
994
views
DESeq2 timecourse experiments
deseq2 timecourse
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
3
replies
1.0k
views
RNA seq time course design using DESeq2
deseq2 timecourse
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
2
replies
1.1k
views
maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
2
votes
3
replies
1.0k
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
0
votes
3
replies
1.2k
views
DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
5.2 years ago cp1015 • 0
4
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18
replies
26k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 5.5 years ago by • 0 • written 10.1 years ago by ▴ 100
0
votes
3
replies
1.3k
views
Is it possible to use DESeq2 likelihood ratio test for time-course analysis to analyse MNase-Seq data?
timecourse mnase-seq deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
vote
5
replies
1.7k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
votes
4
replies
1.4k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
6.3 years ago Maithê Barros ▴ 10
1
vote
1
reply
1.4k
views
Time Series Analysis
timecourse deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 20
0
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0
replies
992
views
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
6.4 years ago rubi ▴ 110
0
votes
3
replies
1.2k
views
time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
1
vote
4
replies
1.5k
views
Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
3
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1.8k
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 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
2
replies
1.4k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
1
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4
replies
2.4k
views
How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
2
votes
4
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1.5k
views
Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 6.9 years ago by • 0 • written 6.9 years ago by • 0
0
votes
0
replies
1.2k
views
Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
7.0 years ago jelisaveta.jeki.djordjevic • 0
0
votes
8
replies
1.8k
views
edgeR: multi-subject time series analysis
timecourse multiple groups edgeR
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 80
0
votes
3
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1.3k
views
How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2 timecourse
updated 7.1 years ago by ★ 13k • written 7.1 years ago by • 0
4
votes
7
replies
2.9k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 7.1 years ago by 43k • written 8.0 years ago by ▴ 10
0
votes
8
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1.8k
views
Time course experiments
deseq2 timecourse
7.2 years ago uu2110 • 0
2
votes
3
replies
2.1k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 2.5 years ago by • 0 • written 7.2 years ago by • 0
6
votes
19
replies
4.2k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 7.2 years ago by ▴ 690 • written 7.2 years ago by ▴ 50
4
votes
8
replies
2.5k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR edger "glmqlftest()" timecourse model
updated 7.4 years ago by ★ 7.9k • written 7.4 years ago by ▴ 10
0
votes
0
replies
1.4k
views
How construct a model for case-control time-course experiment in DEXseq?
dexseq timecourse model.matrix model
7.4 years ago heikki.sarin ▴ 10
3
votes
7
replies
3.3k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 7.4 years ago by ▴ 690 • written 7.4 years ago by • 0
50 results • Page 1 of 1
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Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Hervé Pagès 16k
> I have requested gDNAx developers for a feature request to turn off seqlevelsStyle(txdb) Yes, that's the right course of action. `seqlev…
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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