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
0
votes
0
replies
87
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
11 days ago • updated 6 days ago
Sara
• 0
2
votes
5
replies
261
views
get BM error
ensembldb
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
Fara
• 0
2
votes
5
replies
239
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 10 days ago by
James W. MacDonald
65k • written 12 days ago by
bandconductor
• 0
0
votes
0
replies
82
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
11 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
211
views
Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by
Michael Love
41k • written 11 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
325
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
11 days ago • updated 9 days ago
winwater0928
• 0
3
votes
1
reply
310
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 12 days ago by
Michael Love
41k • written 12 days ago by
i.sudbery
▴ 40
1
vote
1
reply
177
views
Citation for edgeR user guide
edgeR
updated 12 days ago by
Gordon Smyth
50k • written 12 days ago by
k___
▴ 30
0
votes
7
replies
697
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 12 days ago
shepherl
3.9k
1
vote
1
reply
111
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
344
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 11 days ago by
swbarnes2
★ 1.3k • written 12 days ago by
Aaliya
• 0
0
votes
0
replies
71
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
12 days ago
info
▴ 10
1
vote
4
replies
207
views
minfi::read.metharray.exp
minfiData
minfi
updated 11 days ago by
Basti
▴ 780 • written 13 days ago by
clacarion
• 0
0
votes
2
replies
244
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
13 days ago • updated 10 days ago
shuwangxinze1996
• 0
1
vote
2
replies
993
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 13 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
163
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 13 days ago by
taur.vil
• 0
3
votes
3
replies
227
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by
Michael Love
41k • written 13 days ago by
WardDeb
• 0
1
vote
4
replies
234
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 13 days ago by
James W. MacDonald
65k • written 17 days ago by
Mirella Aurora
• 0
0
votes
1
reply
126
views
FDR via q-value
qvalue
updated 13 days ago by
James W. MacDonald
65k • written 16 days ago by
John
• 0
0
votes
5
replies
300
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 11 days ago by
James W. MacDonald
65k • written 14 days ago by
Gayatri
• 0
0
votes
2
replies
212
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
16 days ago • updated 13 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 14 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 13 days ago
shepherl
3.9k
1
vote
13
replies
399
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
14 days ago • updated 11 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
82
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
15 days ago
vaxahey107
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
15 days ago • updated 4 days ago
Chris
• 0
0
votes
0
replies
96
views
I am trying to detect alternative splicing.
ASpli
15 days ago
Sebashish
• 0
3
votes
2
replies
215
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 13 days ago by
Guido Hooiveld
★ 3.9k • written 16 days ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
154
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
bas_work
▴ 30
2
votes
2
replies
190
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 16 days ago by
James W. MacDonald
65k • written 17 days ago by
sansan
• 0
1
vote
0
replies
280
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
16 days ago
BioinfGuru
▴ 30
4
votes
6
replies
429
views
FilterByExpr low counts with small sample size
edgeR
18 days ago • updated 13 days ago
Jonathan
▴ 10
0
votes
2
replies
134
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
16 days ago
prity6459
• 0
0
votes
3
replies
191
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 16 days ago by
Gordon Smyth
50k • written 17 days ago by
prity6459
• 0
3
votes
1
reply
177
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 16 days ago by
Gordon Smyth
50k • written 17 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
202
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
17 days ago
sropri
• 0
0
votes
3
replies
165
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 17 days ago by
Alessia
• 0
0
votes
1
reply
155
views
Adding columns to DEXSeqResults object
DEXSeq
updated 17 days ago by
Alejandro Reyes
★ 1.9k • written 19 days ago by
Clyde
• 0
0
votes
0
replies
119
views
Warning while loading DEP package
DEP
updated 17 days ago by
shepherl
3.9k • written 17 days ago by
Namrata
• 0
0
votes
1
reply
136
views
rlog transformation
DESeq2
updated 17 days ago by
Michael Love
41k • written 17 days ago by
ishij9717
• 0
0
votes
1
reply
112
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 17 days ago by
Michael Love
41k • written 17 days ago by
09191919
• 0
1
vote
2
replies
710
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
18 days ago • updated 9 days ago
ussarizona
▴ 10
0
votes
1
reply
133
views
covariate with negative and positive values
DESeq2
updated 17 days ago by
Michael Love
41k • written 19 days ago by
Brynn
• 0
0
votes
1
reply
148
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
quanah.hudson
• 0
1
vote
2
replies
216
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
17 days ago
Le
• 0
1
vote
2
replies
157
views
Error in champ.load(): The following specified files do not exist
ChAMP
18 days ago • updated 17 days ago
Sherin
• 0
0
votes
1
reply
100
views
Input Question for deseq.r
RSeqAn
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Nina
• 0
0
votes
4
replies
236
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
18 days ago • updated 15 days ago
lonn
• 0
0
votes
7
replies
317
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
18 days ago • updated 12 days ago
hortense96
• 0
0
votes
0
replies
80
views
News:
Services
flowBeads
18 days ago
creativepeptides2018
• 0
1,000 results • Page
2 of 20
Recent ...
Replies
Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
by
Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
Awards
• All
Scholar
to
ATpoint
★ 4.1k
Popular Question
to
Ben
▴ 50
Popular Question
to
Sam
▴ 10
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Zainab
▴ 10
Locations
• All
WEHI, Melbourne, Australia,
2 minutes ago
United States,
27 minutes ago
France,
28 minutes ago
United States,
1 hour ago
Melbourne, Australia,
1 hour ago
Traffic: 465 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