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TimeCourse
•
reset
0
votes
11
replies
349
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
15 days ago • updated 10 days ago
Denise
• 0
0
votes
8
replies
431
views
How to use limma to analyze complex temporal RNAseq data
timecourse
RNASeq
limma
27 days ago • updated 23 days ago
Jiahao Tian
• 0
0
votes
1
reply
704
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 5 months ago by
ATpoint
★ 4.9k • written 5 months ago by
Cosmic
• 0
0
votes
1
reply
476
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 9 months ago by
Michael Love
43k • written 9 months ago by
Jason
• 0
2
votes
4
replies
778
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
10 months ago
jihoon.kim.1495
▴ 10
1
vote
3
replies
981
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 15 months ago by
Gordon Smyth
52k • written 15 months ago by
Ashley
• 0
0
votes
2
replies
910
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
joshua.mannheimer
• 0
0
votes
1
reply
694
views
Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2
timecourse
time
updated 19 months ago by
Michael Love
43k • written 19 months ago by
Anastasiia
• 0
0
votes
1
reply
715
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
20 months ago
WS
• 0
1
vote
6
replies
3.6k
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 8.8 years ago by
Camila Orellana
▴ 10
1
vote
6
replies
3.2k
views
Time-series RNA-seq analysis using DESeq2
time-series
DESeq2
RNASeq
timecoursedata
TimeCourse
updated 2.0 years ago by
ATpoint
★ 4.9k • written 2.0 years ago by
Debebe
• 0
2
votes
1
reply
1.2k
views
DESeq2 time course using fitted splines
RNASeqData
TimeCourse
DESeq2
timecoursedata
updated 14 months ago by
Michael Love
43k • written 2.1 years ago by
georgii.vdovin
• 0
4
votes
5
replies
3.7k
views
DESeq2, time-course interpretation
Transcriptomics
TimeCourse
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.2 years ago by
smac_head
• 0
0
votes
1
reply
987
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 2.2 years ago by
Michael Love
43k • written 2.3 years ago by
Fred
• 0
0
votes
1
reply
963
views
Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2
time-series
timecoursedata
timecourse
multifactorial
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
arshad1292
• 0
3
votes
2
replies
1.5k
views
time-series analysis using EdgeR
timecourse
edgeR
updated 3.3 years ago by
Gordon Smyth
52k • written 3.3 years ago by
Mug_qd
• 0
0
votes
2
replies
3.5k
views
Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse
DESeq2
updated 3.3 years ago by
jeroen.gilis
▴ 100 • written 3.3 years ago by
Maria
• 0
0
votes
1
reply
1.1k
views
DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse
DESeq2
Manual
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
mat.lesche
▴ 110
0
votes
1
reply
954
views
Need of some clarifications
TimeCourse
DifferentialExpression
DESeq2
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
AZ
▴ 30
0
votes
3
replies
1.4k
views
DEseq2 extracting results from multifactor design
timecourse
DESeq2
RNASeq
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
Akhil
• 0
5
votes
9
replies
2.2k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR
RNASeq
DifferentialExpression
TimeCourse
updated 4.1 years ago by
James W. MacDonald
68k • written 4.1 years ago by
svlachavas
▴ 840
0
votes
2
replies
992
views
extracting within time-point differences from time-series model
DESeq2
TimeCourse
4.3 years ago
serpalma.v
▴ 60
0
votes
2
replies
1.3k
views
time couse RNAseq experiment 2 treatments x 4 times
edgeR
timecourse
4.5 years ago
Lina
▴ 10
0
votes
2
replies
1.2k
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR
TimeCourse
RNASeq
updated 4.5 years ago by
Gordon Smyth
52k • written 4.5 years ago by
Lina
▴ 10
1
vote
1
reply
3.6k
views
DESeq2 time course analysis
DESeq2
Timecourse
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
K.
• 0
34
votes
29
replies
16k
views
[DESeq2] time series strain-specific differences over time
deseq2
timecourse
updated 11 months ago by
Michael Love
43k • written 10.5 years ago by
john
▴ 130
1
vote
1
reply
1.2k
views
DESeq2 timecourse experiments
deseq2
timecourse
updated 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
sconosciuto
• 0
0
votes
3
replies
1.2k
views
RNA seq time course design using DESeq2
deseq2
timecourse
updated 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
jackiesalzbank
• 0
0
votes
2
replies
1.3k
views
maSigPro Influential genes, step.methods and gene removal
maSigPro
TimeCourse
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
DcL-A
• 0
2
votes
3
replies
1.2k
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq
Paired design
Timecourse
Diagnosis
Covariates
updated 5.5 years ago by
Kevin Blighe
★ 4.0k • written 5.5 years ago by
ibrahim.akkouh
• 0
0
votes
3
replies
1.4k
views
DESeq2 time course with two genotypes
deseq2
timecourse
michael love
multiple time points
5.9 years ago
cp1015
• 0
4
votes
18
replies
27k
views
DEseq2 time-series design.
deseq2
timecourse
design
updated 6.2 years ago by
simon baldwin
• 0 • written 10.8 years ago by
shao
▴ 100
0
votes
3
replies
1.5k
views
Is it possible to use DESeq2 likelihood ratio test for time-course analysis to analyse MNase-Seq data?
timecourse
mnase-seq
deseq2
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
santos.migueldm
• 0
1
vote
5
replies
2.0k
views
Timecourse gene expression analysis with DESeq2
timecourse
deseq2
multiple factor design
LRT
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
juditkovacsbio
• 0
2
votes
4
replies
1.7k
views
RNA-seq time course experiment - LRT design hep
deseq2
lrt
timecourse
7.0 years ago
Maithê Barros
▴ 10
1
vote
1
reply
1.6k
views
Time Series Analysis
timecourse
deseq2
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
CE
▴ 20
0
votes
0
replies
1.1k
views
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge
differential gene expression
timecourse
interaction
7.1 years ago
rubi
▴ 110
0
votes
3
replies
1.4k
views
time series RNA-seq allowing time offset between individuals
edgeR
deseq2
rna-seq
timecourse
fittimeseries
updated 7.1 years ago by
Aaron Lun
★ 29k • written 7.1 years ago by
jpsf
• 0
1
vote
4
replies
1.7k
views
Analysis Time course data using DESeq2
deseq2
timecourse
multiple time points
time-series
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
zhangfei-123
• 0
2
votes
3
replies
2.0k
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 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
ap874
• 0
2
votes
2
replies
1.6k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger
single cell
design and contrast matrix
timecourse
updated 7.3 years ago by
Gordon Smyth
52k • written 7.3 years ago by
regan.hayward
• 0
1
vote
4
replies
2.7k
views
How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger
differential expression
timecourse
updated 7.5 years ago by
Gordon Smyth
52k • written 7.5 years ago by
Enzo Castillejos
• 0
2
votes
4
replies
1.8k
views
Standard error of log2FC from DESeq in time series experiment
deseq2
log2fc
standard error
timecourse
updated 7.6 years ago by
ellascottgm
• 0 • written 7.6 years ago by
Verena
• 0
0
votes
0
replies
1.4k
views
Understanding NextMaSigPro, regression fit and stepwise regression
timecourse
rnaseq
masigpro
7.7 years ago
jelisaveta.jeki.djordjevic
• 0
0
votes
8
replies
2.2k
views
edgeR: multi-subject time series analysis
timecourse
multiple groups
edgeR
updated 7.8 years ago by
Aaron Lun
★ 29k • written 7.8 years ago by
BharathAnanth
▴ 80
0
votes
3
replies
1.5k
views
How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2
timecourse
updated 7.8 years ago by
Wolfgang Huber
★ 13k • written 7.8 years ago by
Roula
• 0
4
votes
7
replies
3.4k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2
GLM
timecourse
updated 7.8 years ago by
Michael Love
43k • written 8.7 years ago by
rahel14350
▴ 10
0
votes
8
replies
2.1k
views
Time course experiments
deseq2
timecourse
7.8 years ago
uu2110
• 0
2
votes
3
replies
2.4k
views
What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
deseq2
timecourse
updated 3.2 years ago by
chm
• 0 • written 7.9 years ago by
santos.migueldm
• 0
6
votes
19
replies
4.9k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2
timecourse
multiple factor design
RNAseq analysis
differential gene expression
updated 7.9 years ago by
Gavin Kelly
▴ 690 • written 7.9 years ago by
c.nicole
▴ 50
121 results • Page
1 of 3
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0
by
littlefishes20
▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel
by
James W. MacDonald
68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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