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degseq
•
reset
2
votes
5
replies
1.1k
views
Create the design matrix
DEGseq
edgeR
RNASeq
16 months ago
Mohammad
• 0
1
vote
4
replies
919
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
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
1
vote
2
replies
814
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
0
replies
925
views
A question on baySeq
Normalization
DEGseq
DESeq
Normalization
DEGseq
DESeq
13.8 years ago
sunghee OH
▴ 50
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
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
4.1k
views
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
0
replies
1.3k
views
NGS public data analysis
Transcription
DEGseq
Transcription
DEGseq
11.6 years ago
Jill Pleasance
▴ 10
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 11.2 years ago by
delhomme@embl.de
★ 1.2k • written 11.2 years ago by
Guest User
★ 13k
0
votes
0
replies
913
views
Regarding q-value
DEGseq
DEGseq
10.9 years ago
deepika lakhwani
▴ 170
0
votes
0
replies
1.1k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
14.5 years ago
Likun Wang
▴ 50
0
votes
3
replies
1.1k
views
DeSeq2- design experiment
rnaseq
degseq
6.5 years ago
laksharikrish
• 0
0
votes
2
replies
924
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
0
votes
9
replies
536
views
limma fo continous variables
limma
DEGseq
updated 8 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
mia
• 0
0
votes
1
reply
685
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
1
reply
861
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
2
replies
696
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
2
replies
562
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
0
replies
849
views
Extracting gene lists per timepoints using DEGPPatterns package and LRT
DEGseq
clusterProfiler
DEGreport
17 months ago
Rob
• 0
0
votes
1
reply
495
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
★ 4.0k • written 8 months ago by
sybyun419
• 0
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
1.7k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
updated 14.5 years ago by
Ulrike Goebel
▴ 110 • written 14.5 years ago by
Naomi Altman
★ 6.0k
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
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
27 results • Page
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Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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