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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 14.5 years ago by
Ulrike Goebel
▴ 110 • written 14.5 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 11.2 years ago by
delhomme@embl.de
★ 1.2k • written 11.2 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
12.1 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
1.1k
views
Create the design matrix
DEGseq
edgeR
RNASeq
15 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 13.7 years ago by
Simon Anders
★ 3.7k • written 13.7 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
14.5 years ago
Likun Wang
▴ 50
0
votes
0
replies
922
views
A question on baySeq
Normalization
DEGseq
DESeq
Normalization
DEGseq
DESeq
13.7 years ago
sunghee OH
▴ 50
0
votes
2
replies
916
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 21 months ago by
swbarnes2
★ 1.3k • written 21 months ago by
ac.mainul.mmb
• 0
0
votes
0
replies
913
views
Regarding q-value
DEGseq
DEGseq
10.8 years ago
deepika lakhwani
▴ 170
1
vote
4
replies
905
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
1
reply
858
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
839
views
Extracting gene lists per timepoints using DEGPPatterns package and LRT
DEGseq
clusterProfiler
DEGreport
17 months ago
Rob
• 0
1
vote
2
replies
808
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
692
views
RNA-Seq Reads Count
DESeq2
htseq
DEGseq
RNASeq
read
updated 17 months ago by
Michael Love
41k • written 18 months ago by
Paola
• 0
0
votes
1
reply
681
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
553
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
509
views
limma fo continous variables
limma
DEGseq
updated 7 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
mia
• 0
0
votes
1
reply
487
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
27 results • Page
1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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★ 3.2k
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James W. MacDonald
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shepherl
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Gordon Smyth
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