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degseq
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RNA-seq analysis and two-way ANOVAs
edgeR
baySeq
DEGseq
DESeq
DEXSeq
edgeR
baySeq
DEGseq
DESeq
DEXSeq
updated 11.7 years ago by
Gordon Smyth
50k • written 11.7 years ago by
Elena Sorokin
▴ 150
0
votes
8
replies
2.0k
views
Experimental design for RNA-Seq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 13.9 years ago by
Naomi Altman
★ 6.0k • written 13.9 years ago by
michael watson IAH-C
★ 3.4k
0
votes
3
replies
1.7k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
updated 14.6 years ago by
Ulrike Goebel
▴ 110 • written 14.6 years ago by
Naomi Altman
★ 6.0k
0
votes
3
replies
1.4k
views
Analysis of public GEO datasets - NGS
DEGseq
DEGseq
updated 11.6 years ago by
Aliaksei Holik
▴ 350 • written 11.6 years ago by
Guest User
★ 13k
0
votes
1
reply
1.4k
views
Problems in running easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
updated 11.3 years ago by
delhomme@embl.de
★ 1.2k • written 11.3 years ago by
Guest User
★ 13k
1
vote
7
replies
1.4k
views
how to make a contrast of uniquely DE genes
edgeR
limma
RNA-seq
DEGseq
3.1 years ago
decppced
• 0
0
votes
0
replies
1.3k
views
NGS public data analysis
Transcription
DEGseq
Transcription
DEGseq
11.6 years ago
Jill Pleasance
▴ 10
0
votes
1
reply
1.2k
views
Problem with DEGseq/samWrapper
degseq
updated 6.9 years ago by
ab.tsubaki
• 0 • written 9.4 years ago by
jovel_juan
▴ 30
0
votes
3
replies
1.2k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
12.2 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.2k
views
FDR (False Discovery Rate)
baySeq
DEGseq
baySeq
DEGseq
12.2 years ago
Tina Asante Boahene
▴ 100
2
votes
5
replies
1.2k
views
Create the design matrix
DEGseq
edgeR
RNASeq
16 months ago
Mohammad
• 0
0
votes
3
replies
1.1k
views
DeSeq2- design experiment
rnaseq
degseq
6.5 years ago
laksharikrish
• 0
0
votes
0
replies
1.1k
views
DEGseq help
baySeq
DEGseq
baySeq
DEGseq
12.2 years ago
Tina Asante Boahene
▴ 100
0
votes
1
reply
1.1k
views
A question on DESeq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 13.8 years ago by
Simon Anders
★ 3.7k • written 13.8 years ago by
sunghee OH
▴ 50
0
votes
0
replies
1.1k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
14.6 years ago
Likun Wang
▴ 50
0
votes
0
replies
932
views
A question on baySeq
Normalization
DEGseq
DESeq
Normalization
DEGseq
DESeq
13.8 years ago
sunghee OH
▴ 50
0
votes
2
replies
931
views
Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression
GeneExpression
R
enrichment
DEGseq
updated 22 months ago by
swbarnes2
★ 1.3k • written 22 months ago by
ac.mainul.mmb
• 0
1
vote
4
replies
925
views
How to figure out the FC value from Limma
limma
DEGseq
DifferentialExpression
updated 23 months ago by
Kevin Blighe
★ 3.9k • written 23 months ago by
beslinail
• 0
0
votes
0
replies
918
views
Regarding q-value
DEGseq
DEGseq
10.9 years ago
deepika lakhwani
▴ 170
0
votes
1
reply
872
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar
DEGseq
MicroarrayData
updated 2.4 years ago by
James W. MacDonald
65k • written 2.4 years ago by
biomyscience
• 0
0
votes
0
replies
854
views
Extracting gene lists per timepoints using DEGPPatterns package and LRT
DEGseq
clusterProfiler
DEGreport
18 months ago
Rob
• 0
1
vote
2
replies
821
views
DESeq2 desing formula for cell fraction and siRNA scramble
DEGseq
DESeq2
Designformula
updated 3.0 years ago by
swbarnes2
★ 1.3k • written 3.0 years ago by
Nicolò
• 0
0
votes
2
replies
704
views
RNA-Seq Reads Count
DESeq2
htseq
DEGseq
RNASeq
read
updated 18 months ago by
Michael Love
41k • written 18 months ago by
CP
• 0
0
votes
1
reply
692
views
Meta analysis
DEGseq
Metanalysis
updated 2.5 years ago by
Kevin Blighe
★ 3.9k • written 2.5 years ago by
biomyscience
• 0
0
votes
2
replies
576
views
RNA seq differential expression analysis
DEGseq
RNASeqData
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Shaimaa Gamal
• 0
0
votes
9
replies
559
views
limma fo continous variables
limma
DEGseq
updated 9 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
mia
• 0
0
votes
1
reply
502
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData
DEGseq
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
sybyun419
• 0
27 results • Page
1 of 1
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Replies
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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