Showing : Timecourse • reset
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
18
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24
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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
9
votes
7
replies
9.2k
views
DESeq2 timecourse - How to set the experimental design
deseq2 geneexpression timecourse
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 10
7
votes
9
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7.0k
views
DESeq2 time series analysis
DESEQ2 timecourse multiple time points time
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 10
1
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1
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5.5k
views
Mfuzz: fill.NA - Warning messages: argument is not numeric or logical: returning NA
mfuzz clustering bioinformatics proteomics timecourse
updated 8.2 years ago by 1.6k • written 8.2 years ago by • 0
0
votes
1
reply
4.4k
views
Error in contrast.fit, LIMMA
TimeCourse timecourse TimeCourse timecourse
updated 15.2 years ago by ★ 1.1k • written 15.2 years ago by ▴ 10
2
votes
4
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4.4k
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LIMMA on matched time series data
timecourse limma
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 40
1
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11
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4.3k
views
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
6
votes
19
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3.6k
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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
2
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3
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3.3k
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Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
0
votes
5
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3.3k
views
coefficients meaning in time course analysis with DESeq2
deseq2 timecourse time course design and contrast matrix coefficient of variation
updated 8.5 years ago by 41k • written 8.5 years ago by ★ 1.5k
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
1
vote
1
reply
3.0k
views
DESeq2 time series
deseq2 timecourse
updated 7.8 years ago by 41k • written 7.8 years ago by • 0
1
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3
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2.9k
views
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
3
votes
7
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2.9k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 6.7 years ago by ▴ 680 • written 6.7 years ago by • 0
0
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1
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2.7k
views
DESeq: computing 95% CI for negative binomial distribution ?
TimeCourse timecourse DESeq TimeCourse timecourse DESeq
updated 11.0 years ago by 41k • written 11.0 years ago by ▴ 50
0
votes
7
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2.7k
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DESEQ ANODEV : A time course study
TimeCourse timecourse DESeq edgeR
updated 9.3 years ago by 50k • written 10.9 years ago by ▴ 20
3
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4
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2.7k
views
Bioconductor vignette on Time course experiments only describes how to plot the the gene with the smallest p-value. How can I plot specific genes of …
timecourse time course rna-seq deseq2 ggplot2
8.6 years ago moldach ▴ 20
1
vote
6
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2.6k
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 7.4 years ago by ▴ 10
4
votes
7
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2.6k
views
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
4
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6
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2.6k
views
Timecourse Differential expression with multiple factors
deseq2 edger timecourse
7.1 years ago anna_stavrinides ▴ 20
0
votes
3
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2.5k
views
Inherits(x,"data.frame") error in SamR
Microarray Normalization Preprocessing Bayesian Clustering TimeCourse Cancer affy vsn LPE
18.2 years ago McGee, Monnie ▴ 300
1
vote
1
reply
2.5k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 3.2 years ago by 41k • written 3.3 years ago by • 0
1
vote
4
replies
2.1k
views
DEXSeq continous variable in model
RNASeq TimeCourse timecourse DEXSeq DESeq2 RNASeq TimeCourse timecourse DEXSeq DESeq2
updated 9.7 years ago by ★ 1.9k • written 9.7 years ago by ▴ 650
6
votes
5
replies
2.1k
views
Limma : design and contrast for a timecourse experiment with 2 cell lines
limma limma design matrix timecourse
8.3 years ago Pierre-François Roux • 0
1
vote
4
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2.1k
views
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
0
votes
1
reply
2.1k
views
trying to use ballgown with Sailfish/Salmon pipeline
rnaseq multi-mapped reads ballgown salmon timecourse
8.8 years ago friederike.mgh • 0
4
votes
8
replies
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
votes
10
replies
2.0k
views
advice on limma design when analyzing for final outcome in timecourse data
limma timecourse
updated 9.5 years ago by ▴ 20 • written 9.5 years ago by ▴ 220
3
votes
3
replies
1.9k
views
DESeq2 time series: error while measuring gene dispersion.
deseq2 timecourse
updated 9.2 years ago by 41k • written 9.2 years ago by ▴ 40
2
votes
3
replies
1.9k
views
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
votes
2
replies
1.8k
views
Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 22 months ago by ▴ 90 • written 23 months ago by • 0
2
votes
5
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1.8k
views
DESeq2 time series tissue specific differences over time
deseq2 timecourse multiple time points rnaseq
6.8 years ago Nicholas Owen • 0
5
votes
2
replies
1.8k
views
DESeq2 design matrix for timecourse
deseq2 experimental design timecourse rnaseq model
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 20
2
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3
replies
1.7k
views
Deseq2 time series question,
rnaseq deseq2 timecourse
updated 7.4 years ago by 41k • written 7.4 years ago by • 0
0
votes
1
reply
1.7k
views
filtering Gene 1.0 ST chips
TimeCourse probe timecourse oligo TimeCourse probe timecourse oligo
updated 11.2 years ago by ▴ 910 • written 11.2 years ago by ▴ 10
0
votes
3
replies
1.7k
views
Timeseries loop design analysis using Limma or Maanova?
Bayesian Clustering TimeCourse timecourse oligo Bayesian Clustering TimeCourse timecourse
18.2 years ago Pete ▴ 70
0
votes
7
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1.6k
views
data preparation for timecourse
timecourse
updated 9.4 years ago by ★ 1.5k • written 9.4 years ago by • 0
0
votes
10
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1.6k
views
Timecourse package
Microarray TimeCourse timecourse Microarray TimeCourse timecourse
updated 15.2 years ago by ▴ 440 • written 15.2 years ago by ▴ 380
0
votes
8
replies
1.6k
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Time course experiments
deseq2 timecourse
6.5 years ago uu2110 • 0
0
votes
8
replies
1.6k
views
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
votes
1
reply
1.6k
views
RNASeq time-course analysis with maSigPro: T.fit error when assessing multiple groups
rnaseq masigpro timecourse
9.0 years ago Ryan Goosen • 0
7
votes
5
replies
1.6k
views
Which is the best design matrix to compare a timecourse between two conditions?
limma voom design matrix timecourse
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 10
5
votes
9
replies
1.5k
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
4
votes
6
replies
1.5k
views
Multi-factorial design for patient-replicates from different time points (Deseq2)
deseq2 rnaseq timecourse multiple time points multifactorial design
updated 7.1 years ago by 41k • written 7.1 years ago by • 0
2
votes
3
replies
1.5k
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 5.8 years ago by 41k • written 5.8 years ago by • 0
0
votes
4
replies
1.5k
views
using timecourse package with non-replicated time course
Microarray TimeCourse timecourse Microarray TimeCourse timecourse
updated 12.8 years ago by ▴ 440 • written 12.8 years ago by ▴ 30
1
vote
5
replies
1.4k
views
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
0
votes
3
replies
1.4k
views
timecourse + factorial + replicates in LIMMA
TimeCourse timecourse TimeCourse timecourse
updated 16.6 years ago by ★ 6.0k • written 16.6 years ago by ▴ 70
1
vote
6
replies
1.4k
views
edgeR time series DMSO correction
edger makecontrasts timecourse
updated 7.4 years ago by ★ 7.9k • written 7.4 years ago by ▴ 90
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Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Comment: Error retrieving ensembl gene id using biomaRt... by James W. MacDonald 65k
Or that. ;-D
Answer: Error retrieving ensembl gene id using biomaRt... by Mike Smith ★ 6.5k
I think you have the assignment operator (`<-`) the wrong way round. It should be `df_biomrt_tmp <- getBM(...`
Answer: Error retrieving ensembl gene id using biomaRt... by James W. MacDonald 65k
I can't reproduce. ``` > library(biomaRt) Warning message: package 'biomaRt' was built under R version 4.3.2 > library(org.Hs.eg.db…
Comment: DESeq2 setting significant p-value by Michael Love 41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
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Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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