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
2
replies
915
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
4
votes
8
replies
386
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 14 days ago by
Peter Hickey
▴ 740 • written 21 days ago by
Juan Higareda
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 14 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
187
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
14 days ago
sropri
• 0
1
vote
2
replies
208
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
14 days ago
Le
• 0
0
votes
3
replies
249
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 14 days ago by
W. Evan Johnson
▴ 850 • written 20 days ago by
schlumbohm
• 0
0
votes
0
replies
114
views
Warning while loading DEP package
DEP
updated 14 days ago by
shepherl
3.9k • written 14 days ago by
Namrata
• 0
0
votes
1
reply
147
views
Adding columns to DEXSeqResults object
DEXSeq
updated 14 days ago by
Alejandro Reyes
★ 1.9k • written 16 days ago by
Clyde
• 0
0
votes
1
reply
123
views
rlog transformation
DESeq2
updated 14 days ago by
Michael Love
41k • written 14 days ago by
ishij9717
• 0
0
votes
1
reply
106
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 14 days ago by
Michael Love
41k • written 14 days ago by
09191919
• 0
0
votes
1
reply
128
views
covariate with negative and positive values
DESeq2
updated 14 days ago by
Michael Love
41k • written 16 days ago by
Brynn
• 0
1
vote
2
replies
150
views
Error in champ.load(): The following specified files do not exist
ChAMP
15 days ago • updated 14 days ago
Sherin
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 14 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
899
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
22 days ago • updated 14 days ago
Chris
• 0
0
votes
1
reply
98
views
Input Question for deseq.r
RSeqAn
updated 14 days ago by
ATpoint
★ 4.1k • written 15 days ago by
Nina
• 0
0
votes
1
reply
139
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 days ago by
ATpoint
★ 4.1k • written 15 days ago by
quanah.hudson
• 0
3
votes
3
replies
196
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
20 days ago • updated 14 days ago
jacques.imbert
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 14 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 15 days ago
shepherl
3.9k
0
votes
2
replies
907
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 15 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 15 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 15 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
0
replies
73
views
News:
Services
flowBeads
15 days ago
creativepeptides2018
• 0
0
votes
0
replies
77
views
Enzyme Engineering
BioTIP
15 days ago
bocchemistry
• 0
0
votes
0
replies
76
views
News:
TIDES USA 2024
flowBeads
15 days ago
bocsci11
• 0
0
votes
0
replies
88
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
16 days ago
Maliha Tabassum
• 0
0
votes
4
replies
592
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 16 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
4
replies
182
views
flowStats Search Error
flowStats
updated 16 days ago by
shepherl
3.9k • written 17 days ago by
tholmes
• 0
0
votes
1
reply
135
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 16 days ago by
James W. MacDonald
65k • written 19 days ago by
tian.liu0720
• 0
1
vote
2
replies
131
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
16 days ago
Ana
• 0
0
votes
1
reply
118
views
what is the sampleFiles
chipseq
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
zhulin
• 0
0
votes
3
replies
200
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by
Michael Love
41k • written 17 days ago by
andrebolerbarros
▴ 20
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
1
vote
1
reply
182
views
Differentially expressed genes in monocle pseudotime
monocle
updated 16 days ago by
Gordon Smyth
50k • written 18 days ago by
kthapa
• 0
2
votes
2
replies
166
views
[DiffBind] Obtaining normalization factors
DiffBind
20 days ago • updated 16 days ago
Henry
▴ 10
2
votes
3
replies
319
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
17 days ago • updated 16 days ago
daniel.carbajo
• 0
0
votes
1
reply
136
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 16 days ago by
kamryncole1963
• 0 • written 21 days ago by
Sara
• 0
0
votes
4
replies
5.2k
views
SingleR Label.Ont
SingleR
updated 17 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
0
replies
93
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
17 days ago
Virangika
• 0
0
votes
0
replies
70
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
17 days ago
Henry
▴ 10
1
vote
2
replies
486
views
GSVA error
GSVA
18 days ago • updated 17 days ago
Alex
• 0
0
votes
1
reply
128
views
Deseq2 Rlog transformation
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Sahar
• 0
1
vote
3
replies
343
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 17 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
2
votes
2
replies
167
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
20 days ago • updated 17 days ago
daniel.carbajo
• 0
0
votes
1
reply
157
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 18 days ago by
Guido Hooiveld
★ 3.9k • written 22 days ago by
Lucie
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 18 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
1
vote
2
replies
189
views
Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago
hemantcnaik
• 0
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 19 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
5
votes
6
replies
415
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 19 days ago by
ATpoint
★ 4.1k • written 23 days ago by
nhaus
▴ 30
2
votes
2
replies
188
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
20 days ago
julia_mcdonough
• 0
1,744 results • Page
3 of 35
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
Awards
• All
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Popular Question
to
shepherl
3.9k
Popular Question
to
siajunren
• 0
Scholar
to
Rory Stark
★ 5.2k
Locations
• All
WEHI, Melbourne, Australia,
2 minutes ago
France,
4 minutes ago
St Louis, MO,
35 minutes ago
United States,
1 hour ago
United States,
2 hours ago
Traffic: 595 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