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
1
vote
2
replies
203
views
Citation for edgeR user guide
edgeR
written 24 days ago by
k___
▴ 30
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by
Michael Love
42k • written 24 days ago by
i.sudbery
▴ 40
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
383
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 23 days ago by
swbarnes2
★ 1.4k • written 24 days ago by
Aaliya
• 0
0
votes
0
replies
82
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
24 days ago
info
▴ 10
0
votes
2
replies
265
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
25 days ago • updated 23 days ago
shuwangxinze1996
• 0
0
votes
2
replies
190
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 25 days ago by
taur.vil
• 0
3
votes
3
replies
250
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 24 days ago by
Michael Love
42k • written 25 days ago by
WardDeb
• 0
1
vote
4
replies
229
views
minfi::read.metharray.exp
minfiData
minfi
updated 24 days ago by
Basti
▴ 780 • written 25 days ago by
clacarion
• 0
1
vote
2
replies
212
views
Improving the design matrices vignette in RNAseq123
RNAseq123
26 days ago • updated 11 days ago
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
324
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 23 days ago by
James W. MacDonald
65k • written 26 days ago by
Gayatri
• 0
2
votes
13
replies
477
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
26 days ago • updated 23 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
94
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
27 days ago
vaxahey107
• 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
27 days ago • updated 16 days ago
Chris
▴ 10
0
votes
0
replies
105
views
I am trying to detect alternative splicing.
ASpli
27 days ago
Sebashish
• 0
3
votes
2
replies
229
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 25 days ago by
Guido Hooiveld
★ 4.0k • written 28 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 25 days ago by
James W. MacDonald
65k • written 28 days ago by
John
• 0
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
28 days ago • updated 26 days ago
catv
• 0
0
votes
3
replies
173
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
bas_work
▴ 30
1
vote
0
replies
348
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
28 days ago
BioinfGuru
▴ 30
0
votes
2
replies
147
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
29 days ago
prity6459
• 0
2
votes
2
replies
212
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 28 days ago by
James W. MacDonald
65k • written 29 days ago by
sansan
• 0
0
votes
4
replies
216
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
29 days ago
sropri
• 0
2
votes
4
replies
280
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 25 days ago by
James W. MacDonald
65k • written 29 days ago by
Mirella Aurora
• 0
0
votes
3
replies
210
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 29 days ago by
Gordon Smyth
50k • written 29 days ago by
prity6459
• 0
0
votes
0
replies
132
views
Warning while loading DEP package
DEP
updated 29 days ago by
shepherl
3.9k • written 29 days ago by
Namrata
• 0
0
votes
3
replies
187
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 17 days ago by
Alejandro Reyes
★ 1.9k • written 29 days ago by
Alessia
• 0
0
votes
1
reply
157
views
rlog transformation
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
0
votes
1
reply
125
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 8 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
1
vote
2
replies
235
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
4 weeks ago • updated 29 days ago
Le
• 0
1
vote
2
replies
178
views
Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago • updated 29 days ago
Sherin
• 0
0
votes
1
reply
111
views
Input Question for deseq.r
RSeqAn
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Nina
• 0
4
votes
6
replies
469
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 25 days ago
Jonathan
▴ 10
0
votes
4
replies
263
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 28 days ago
lonn
• 0
1
vote
2
replies
738
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 21 days ago
Patadù
▴ 10
0
votes
1
reply
166
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
0
votes
7
replies
362
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 25 days ago
hortense96
• 0
0
votes
0
replies
95
views
News:
Services
flowBeads
4 weeks ago
creativepeptides2018
• 0
0
votes
0
replies
91
views
Enzyme Engineering
BioTIP
4 weeks ago
bocchemistry
• 0
0
votes
0
replies
96
views
News:
TIDES USA 2024
flowBeads
4 weeks ago
bocsci11
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
1
reply
166
views
Adding columns to DEXSeqResults object
DEXSeq
updated 29 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
0
votes
0
replies
105
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
4 weeks ago
Maliha Tabassum
• 0
1
vote
2
replies
171
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
4 weeks ago
Ana
• 0
0
votes
1
reply
135
views
what is the sampleFiles
chipseq
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
zhulin
• 0
0
votes
4
replies
218
views
flowStats Search Error
flowStats
updated 4 weeks ago by
shepherl
3.9k • written 4 weeks ago by
tholmes
• 0
0
votes
0
replies
105
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 weeks ago
Virangika
• 0
0
votes
0
replies
82
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 weeks ago
Henry
▴ 10
0
votes
3
replies
229
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
andrebolerbarros
▴ 20
1,000 results • Page
3 of 20
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards
• All
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
Koen Van den Berge
▴ 180
Popular Question
to
shepherl
3.9k
Popular Question
to
Ken C
• 0
Popular Question
to
Johannes Rainer
★ 2.0k
Locations
• All
WEHI, Melbourne, Australia,
12 minutes ago
India,
1 hour ago
Greece,
2 hours ago
Poland,
2 hours ago
United States,
3 hours ago
Traffic: 440 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