Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 4 hours ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 11 hours ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
782
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 12 hours ago
Chris
• 0
4
votes
8
replies
289
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 2 hours ago by
Peter Hickey
▴ 740 • written 7 days ago by
Juan Higareda
• 0
3
votes
3
replies
133
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
6 days ago • updated 16 hours ago
jacques.imbert
• 0
2
votes
3
replies
633
views
DESeq2 setting significant p-value
DESeq2
updated 12 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
1
vote
2
replies
98
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
18 hours ago • updated 5 hours ago
Le
• 0
1
vote
2
replies
740
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 6 hours ago by
sredemption
• 0 • written 13 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
75
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 day ago • updated 11 hours ago
Sherin
• 0
0
votes
1
reply
35
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 hours ago by
Alejandro Reyes
★ 1.9k • written 14 hours ago by
Alessia
• 0
0
votes
0
replies
22
views
Warning while loading DEP package
DEP
updated 9 hours ago by
shepherl
3.8k • written 9 hours ago by
Namrata
• 0
0
votes
3
replies
185
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 9 hours ago by
W. Evan Johnson
▴ 850 • written 6 days ago by
schlumbohm
• 0
0
votes
2
replies
107
views
FilterByExpr low counts with small sample size
edgeR
1 day ago • updated 9 hours ago
Jonathan
▴ 10
0
votes
0
replies
17
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
8 hours ago
prity6459
• 0
0
votes
0
replies
18
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
8 hours ago
Mirella Aurora
• 0
0
votes
1
reply
49
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 7 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
lonn
• 0
0
votes
4
replies
49
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
6 hours ago • updated 5 hours ago
sropri
• 0
0
votes
1
reply
28
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 3 hours ago by
Guido Hooiveld
★ 3.9k • written 4 hours ago by
sansan
• 0
0
votes
1
reply
56
views
Adding columns to DEXSeqResults object
DEXSeq
updated 9 hours ago by
Alejandro Reyes
★ 1.9k • written 2 days ago by
Clyde
• 0
0
votes
2
replies
271
views
DESeq filtering specific to contrasts
DESeq2
updated 16 hours ago by
Carlin95
• 0 • written 9 weeks ago by
Emma
• 0
0
votes
1
reply
69
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
quanah.hudson
• 0
0
votes
1
reply
48
views
Input Question for deseq.r
RSeqAn
updated 13 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
Nina
• 0
0
votes
1
reply
66
views
covariate with negative and positive values
DESeq2
updated 10 hours ago by
Michael Love
41k • written 2 days ago by
Brynn
• 0
0
votes
1
reply
47
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 10 hours ago by
Michael Love
41k • written 1 day ago by
ussarizona
• 0
0
votes
1
reply
35
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 10 hours ago by
Michael Love
41k • written 16 hours ago by
09191919
• 0
0
votes
1
reply
38
views
rlog transformation
DESeq2
updated 10 hours ago by
Michael Love
41k • written 15 hours ago by
ishij9717
• 0
0
votes
0
replies
34
views
Log-cpm values from limma
limma
edgeR
RNASeq
17 hours ago
Shaimaa Gamal
• 0
27 results • Page
1 of 1
Recent ...
Replies
Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
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
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Awards
• All
Scholar
to
Peter Hickey
▴ 740
Popular Question
to
sropri
• 0
Popular Question
to
W. Evan Johnson
▴ 850
Popular Question
to
Alejandro Reyes
★ 1.9k
Popular Question
to
shepherl
3.8k
Locations
• All
United States,
1 minute ago
United States,
2 minutes ago
Vietnam,
4 minutes ago
United States,
25 minutes ago
France,
29 minutes ago
Traffic: 622 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6