Showing : timecourse • reset
1
vote
6
replies
2.2k
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 6.9 years ago by ▴ 10
1
vote
6
replies
395
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 6 weeks ago by ★ 3.4k • written 6 weeks ago by • 0
0
votes
1
reply
189
views
DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 12 weeks ago by 40k • written 12 weeks ago by • 0
2
votes
5
replies
425
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 11 weeks ago by 40k • written 3 months ago by • 0
0
votes
1
reply
342
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 4 months ago by 40k • written 4 months ago by • 0
0
votes
1
reply
414
views
Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 10 months ago by 40k • written 11 months ago by • 0
3
votes
2
replies
705
views
time-series analysis using EdgeR
timecourse edgeR
updated 16 months ago by 48k • written 16 months ago by • 0
0
votes
2
replies
1.0k
views
Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 16 months ago by ▴ 90 • written 16 months ago by • 0
0
votes
1
reply
513
views
DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 19 months ago by 40k • written 19 months ago by ▴ 90
0
votes
1
reply
553
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 24 months ago by 40k • written 24 months ago by ▴ 30
0
votes
3
replies
747
views
DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 2.1 years ago by 40k • written 2.1 years ago by • 0
5
votes
9
replies
1.3k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.2 years ago by 63k • written 2.2 years ago by ▴ 810
0
votes
2
replies
560
views
extracting within time-point differences from time-series model
DESeq2 TimeCourse
2.4 years ago serpalma.v ▴ 60
0
votes
2
replies
788
views
time couse RNAseq experiment 2 treatments x 4 times
edgeR timecourse
2.6 years ago HS ▴ 10
0
votes
2
replies
709
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 2.6 years ago by 48k • written 2.6 years ago by ▴ 10
1
vote
1
reply
1.8k
views
DESeq2 time course analysis
DESeq2 Timecourse
updated 2.7 years ago by 40k • written 2.7 years ago by • 0
18
votes
24
replies
13k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 2.7 years ago by • 0 • written 8.6 years ago by ▴ 120
1
vote
1
reply
628
views
DESeq2 timecourse experiments
deseq2 timecourse
updated 3.1 years ago by 40k • written 3.1 years ago by • 0
0
votes
3
replies
595
views
RNA seq time course design using DESeq2
deseq2 timecourse
updated 3.1 years ago by 40k • written 3.1 years ago by • 0
0
votes
2
replies
627
views
maSigPro Influential genes, step.methods and gene removal
maSigPro TimeCourse
updated 3.3 years ago by 40k • written 3.3 years ago by • 0
2
votes
3
replies
669
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 3.5 years ago by 3.8k • written 3.5 years ago by • 0
0
votes
3
replies
736
views
DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
4.0 years ago cp1015 • 0
4
votes
18
replies
22k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.3 years ago by • 0 • written 8.9 years ago by ▴ 100
0
votes
3
replies
963
views
Is it possible to use DESeq2 likelihood ratio test for time-course analysis to analyse MNase-Seq data?
timecourse mnase-seq deseq2
updated 4.5 years ago by 40k • written 4.5 years ago by • 0
1
vote
5
replies
1.2k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 4.8 years ago by 40k • written 4.8 years ago by • 0
2
votes
4
replies
958
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
5.0 years ago Maithê Barros ▴ 10
1
vote
1
reply
1.0k
views
Time Series Analysis
timecourse deseq2
updated 5.1 years ago by 40k • written 5.1 years ago by ▴ 20
0
votes
0
replies
711
views
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
5.1 years ago rubi ▴ 110
0
votes
3
replies
797
views
time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
1
vote
4
replies
1.1k
views
Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 5.2 years ago by 40k • written 5.2 years ago by • 0
2
votes
3
replies
1.2k
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 5.3 years ago by 40k • written 5.3 years ago by • 0
2
votes
2
replies
944
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 5.4 years ago by 48k • written 5.4 years ago by • 0
1
vote
4
replies
1.9k
views
How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 5.6 years ago by 48k • written 5.6 years ago by • 0
2
votes
4
replies
1.1k
views
Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 5.6 years ago by • 0 • written 5.7 years ago by • 0
0
votes
0
replies
905
views
Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
5.8 years ago jelisaveta.jeki.djordjevic • 0
0
votes
8
replies
1.4k
views
edgeR: multi-subject time series analysis
timecourse multiple groups edgeR
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 80
0
votes
3
replies
955
views
How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2 timecourse
updated 5.9 years ago by 13k • written 5.9 years ago by • 0
4
votes
7
replies
2.4k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 5.9 years ago by 40k • written 6.8 years ago by ▴ 10
0
votes
8
replies
1.3k
views
Time course experiments
deseq2 timecourse
5.9 years ago uu2110 • 0
2
votes
3
replies
1.6k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2 timecourse
updated 15 months ago by • 0 • written 6.0 years ago by • 0
6
votes
19
replies
3.0k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 6.0 years ago by ▴ 670 • written 6.0 years ago by ▴ 50
4
votes
8
replies
1.8k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR edger "glmqlftest()" timecourse model
updated 6.2 years ago by 7.8k • written 6.2 years ago by ▴ 10
0
votes
0
replies
1.1k
views
How construct a model for case-control time-course experiment in DEXseq?
dexseq timecourse model.matrix model
6.2 years ago heikki.sarin ▴ 10
3
votes
7
replies
2.5k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 6.2 years ago by ▴ 670 • written 6.2 years ago by • 0
2
votes
1
reply
856
views
DEseq2 time-series before and after Infection
multiple factor design deseq2 timecourse
updated 6.2 years ago by 40k • written 6.2 years ago by • 0
2
votes
5
replies
1.5k
views
DESeq2 time series tissue specific differences over time
deseq2 timecourse multiple time points rnaseq
6.3 years ago • updated 6.2 years ago Nicholas Owen • 0
0
votes
2
replies
2.6k
views
Time-course analysis with limma for >3 time points
limma contrast matrix design matrix multiple time points timecourse
updated 2.4 years ago by • 0 • written 6.3 years ago by ▴ 20
7
votes
9
replies
6.6k
views
DESeq2 time series analysis
DESEQ2 timecourse multiple time points time
updated 6.3 years ago by 40k • written 6.3 years ago by ▴ 10
4
votes
6
replies
2.2k
views
Timecourse Differential expression with multiple factors
deseq2 edger timecourse
6.6 years ago • updated 6.5 years ago anna_stavrinides ▴ 20
4
votes
6
replies
1.4k
views
Multi-factorial design for patient-replicates from different time points (Deseq2)
deseq2 rnaseq timecourse multiple time points multifactorial design
updated 6.6 years ago by 40k • written 6.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: tximport error: vroom by Benji Bromberg • 0
Worked perfectly! Thanks!
Comment: tximport error: vroom by Michael Love 40k
You can force the function used for importing: https://github.com/thelovelab/tximport/blob/devel/R/tximport.R#L265 Try `importer=read.del…
Comment: tximport error: vroom by Benji Bromberg • 0
Of course! Let me know if you figure it out.
Comment: tximport error: vroom by RLiu ▴ 10
Thank you for providing this clue. I never installed vroom manually. I guess it is one of dependences for tximport that automatically insta…
Comment: tximport error: vroom by RLiu ▴ 10
I checked that all `quant.sf`s have the same line number (42013 lines in each file), which is different from tx2gene (81493 lines).
Votes
Answer: tximport error: vroom
Comment: tximport error: vroom
tximport error: vroom
Comment: Speeding up of DelayedArray::write_block()
Comment: Speeding up of DelayedArray::write_block()
Awards • All
Popular Question to mattia pelizzola ▴ 200
Popular Question to ayabalbaa1990 • 0
Popular Question to Wolfgang Huber 13k
Popular Question to Yahan • 0
Popular Question to Gordon Smyth 48k
Locations • All
United States, 3 minutes ago
United States, 11 minutes ago
Russia, 19 minutes ago
Canada, 44 minutes ago
United Kingdom, 47 minutes ago
Traffic: 473 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6