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News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 9 hours ago
shepherl
3.8k
6
votes
16
replies
2.2k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 13 hours ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
1
vote
1
reply
37
views
Citation for edgeR user guide
edgeR
updated 5 hours ago by
Gordon Smyth
50k • written 8 hours ago by
k___
▴ 30
1
vote
1
reply
46
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 hour ago by
Michael Love
41k • written 9 hours ago by
i.sudbery
▴ 40
3
votes
3
replies
134
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 13 hours ago by
Michael Love
41k • written 1 day ago by
WardDeb
• 0
1
vote
3
replies
103
views
minfi::read.metharray.exp
minfiData
minfi
1 day ago • updated 7 hours ago
clacarion
• 0
5
votes
8
replies
8.7k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 18 hours ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
1
vote
1
reply
37
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 10 hours ago by
James W. MacDonald
65k • written 11 hours ago by
fernanda.backsouza
▴ 10
0
votes
7
replies
233
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
6 days ago • updated 18 hours ago
hortense96
• 0
0
votes
3
replies
142
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 14 hours ago by
James W. MacDonald
65k • written 2 days ago by
Gayatri
• 0
0
votes
2
replies
42
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
12 hours ago • updated 10 minutes ago
Aaliya
• 0
0
votes
0
replies
19
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
12 hours ago
info
▴ 10
1
vote
11
replies
173
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
2 days ago • updated 10 hours ago
fernanda.backsouza
▴ 10
0
votes
1
reply
34
views
How to retrieve gene ontology GO class?
GO.db
goTools
6 hours ago • updated 5 hours ago
bandconductor
• 0
0
votes
0
replies
26
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
23 hours ago
shuwangxinze1996
• 0
15 results • Page
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Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
by
Michael Love
41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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