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degseq
•
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0
votes
3
replies
312
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Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA
RNASeqPower
DEGseq
written 10 weeks ago by
Jonathan
• 0
0
votes
9
replies
1.5k
views
limma fo continous variables
limma
DEGseq
updated 11 months ago by
James W. MacDonald
67k • written 11 months ago by
mia
• 0
0
votes
1
reply
817
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData
DEGseq
updated 17 months ago by
ATpoint
★ 4.6k • written 17 months ago by
sybyun419
• 0
0
votes
2
replies
777
views
RNA seq differential expression analysis
DEGseq
RNASeqData
limma
updated 19 months ago by
Gordon Smyth
52k • written 19 months ago by
Shaimaa Gamal
• 0
2
votes
5
replies
1.5k
views
Create the design matrix
DEGseq
edgeR
RNASeq
2.1 years ago
Mohammad
• 0
0
votes
0
replies
1.2k
views
Extracting gene lists per timepoints using DEGPPatterns package and LRT
DEGseq
clusterProfiler
DEGreport
2.2 years ago
Rob
• 0
0
votes
2
replies
996
views
RNA-Seq Reads Count
DESeq2
htseq
DEGseq
RNASeq
read
updated 2.2 years ago by
Michael Love
43k • written 2.3 years ago by
CP
• 0
0
votes
2
replies
1.2k
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 2.6 years ago by
swbarnes2
★ 1.4k • written 2.6 years ago by
ac.mainul.mmb
• 0
1
vote
4
replies
1.2k
views
How to figure out the FC value from Limma
limma
DEGseq
DifferentialExpression
updated 2.7 years ago by
Kevin Blighe
★ 4.0k • written 2.7 years ago by
beslinail
• 0
0
votes
1
reply
1.1k
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar
DEGseq
MicroarrayData
updated 3.2 years ago by
James W. MacDonald
67k • written 3.2 years ago by
biomyscience
• 0
0
votes
1
reply
853
views
Meta analysis
DEGseq
Metanalysis
updated 3.3 years ago by
Kevin Blighe
★ 4.0k • written 3.3 years ago by
biomyscience
• 0
1
vote
2
replies
1.0k
views
DESeq2 desing formula for cell fraction and siRNA scramble
DEGseq
DESeq2
Designformula
updated 3.7 years ago by
swbarnes2
★ 1.4k • written 3.7 years ago by
Nicolò
• 0
1
vote
7
replies
1.7k
views
how to make a contrast of uniquely DE genes
edgeR
limma
RNA-seq
DEGseq
3.9 years ago
decppced
• 0
0
votes
3
replies
1.4k
views
DeSeq2- design experiment
rnaseq
degseq
7.3 years ago
laksharikrish
• 0
0
votes
1
reply
1.4k
views
Problem with DEGseq/samWrapper
degseq
updated 7.6 years ago by
ab.tsubaki
• 0 • written 10.2 years ago by
jovel_juan
▴ 30
0
votes
0
replies
1.1k
views
Regarding q-value
DEGseq
DEGseq
11.6 years ago
deepika lakhwani
▴ 170
0
votes
1
reply
1.6k
views
Problems in running easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
updated 12.0 years ago by
delhomme@embl.de
★ 1.2k • written 12.0 years ago by
Guest User
★ 13k
0
votes
3
replies
1.7k
views
Analysis of public GEO datasets - NGS
DEGseq
DEGseq
updated 12.4 years ago by
Aliaksei Holik
▴ 350 • written 12.4 years ago by
Guest User
★ 13k
0
votes
0
replies
1.4k
views
NGS public data analysis
Transcription
DEGseq
Transcription
DEGseq
12.4 years ago
Jill Pleasance
▴ 10
0
votes
1
reply
4.4k
views
RNA-seq analysis and two-way ANOVAs
edgeR
baySeq
DEGseq
DESeq
DEXSeq
edgeR
baySeq
DEGseq
DESeq
DEXSeq
updated 12.4 years ago by
Gordon Smyth
52k • written 12.4 years ago by
Elena Sorokin
▴ 160
0
votes
3
replies
1.3k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
12.9 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.2k
views
DEGseq help
baySeq
DEGseq
baySeq
DEGseq
13.0 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.3k
views
FDR (False Discovery Rate)
baySeq
DEGseq
baySeq
DEGseq
13.0 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.1k
views
A question on baySeq
Normalization
DEGseq
DESeq
Normalization
DEGseq
DESeq
14.5 years ago
sunghee OH
▴ 50
0
votes
1
reply
1.2k
views
A question on DESeq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 14.5 years ago by
Simon Anders
★ 3.8k • written 14.5 years ago by
sunghee OH
▴ 50
0
votes
8
replies
2.3k
views
Experimental design for RNA-Seq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 14.7 years ago by
Naomi Altman
★ 6.0k • written 14.7 years ago by
michael watson IAH-C
★ 3.4k
0
votes
3
replies
1.9k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
updated 15.3 years ago by
Ulrike Goebel
▴ 110 • written 15.3 years ago by
Naomi Altman
★ 6.0k
0
votes
0
replies
1.2k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
15.3 years ago
Likun Wang
▴ 50
28 results • Page
1 of 1
Recent ...
Replies
Comment: input for singR function
by
iamin053
• 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile
by
yf
• 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Votes
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
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