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4
replies
125
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
5 days ago
sropri
• 0
1
vote
2
replies
177
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
5 days ago
Le
• 0
1
vote
2
replies
763
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 5 days ago by
sredemption
• 0 • written 13 months ago by
ruiqi.li
▴ 10
0
votes
3
replies
218
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 5 days ago by
W. Evan Johnson
▴ 850 • written 11 days ago by
schlumbohm
• 0
0
votes
0
replies
84
views
Warning while loading DEP package
DEP
updated 5 days ago by
shepherl
3.8k • written 5 days ago by
Namrata
• 0
0
votes
1
reply
78
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 5 days ago by
Alessia
• 0
0
votes
1
reply
112
views
Adding columns to DEXSeqResults object
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 7 days ago by
Clyde
• 0
0
votes
1
reply
84
views
rlog transformation
DESeq2
updated 5 days ago by
Michael Love
41k • written 5 days ago by
ishij9717
• 0
0
votes
1
reply
83
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 5 days ago by
Michael Love
41k • written 5 days ago by
09191919
• 0
0
votes
1
reply
93
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
ussarizona
• 0
0
votes
1
reply
107
views
covariate with negative and positive values
DESeq2
updated 5 days ago by
Michael Love
41k • written 7 days ago by
Brynn
• 0
1
vote
2
replies
123
views
Error in champ.load(): The following specified files do not exist
ChAMP
6 days ago • updated 5 days ago
Sherin
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 5 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
844
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
13 days ago • updated 5 days ago
Chris
• 0
0
votes
1
reply
77
views
Input Question for deseq.r
RSeqAn
updated 5 days ago by
ATpoint
★ 4.0k • written 6 days ago by
Nina
• 0
0
votes
1
reply
109
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 5 days ago by
ATpoint
★ 4.0k • written 6 days ago by
quanah.hudson
• 0
3
votes
3
replies
164
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
11 days ago • updated 5 days ago
jacques.imbert
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 6 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 6 days ago
shepherl
3.8k
0
votes
2
replies
884
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 6 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 6 days ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 6 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
0
replies
60
views
News:
Services
flowBeads
6 days ago
creativepeptides2018
• 0
0
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0
replies
51
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Enzyme Engineering
BioTIP
6 days ago
bocchemistry
• 0
74 results • Page
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Comment: How to retrieve gene ontology GO class?
by
bandconductor
• 0
Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence. I have …
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?
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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