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
17
votes
4
replies
8.8k
views
Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 3 days ago by
Mj.A.
• 0 • written 5.2 years ago by
shepherl
3.8k
11
votes
4
replies
7.2k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 2 days ago by
Peter Langfelder
★ 2.9k • written 9.0 years ago by
brohawndg
▴ 150
7
votes
6
replies
335
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
Amit
• 0
4
votes
7
replies
331
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 1 day ago by
Gordon Smyth
50k • written 12 days ago by
Amit
• 0
4
votes
3
replies
517
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 1 day ago by
Gordon Smyth
50k • written 8 days ago by
Jack S.
▴ 50
3
votes
2
replies
124
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
4 days ago
Anita
▴ 10
2
votes
1
reply
159
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 4 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Dario Strbenac
★ 1.5k
2
votes
2
replies
112
views
From a DNAStringSet to a data.frame
Biostrings
3 days ago
ramiro.barrantes
▴ 10
2
votes
1
reply
124
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 4 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
enee
▴ 10
2
votes
3
replies
144
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 3 days ago by
Wei Shi
★ 3.6k • written 4 days ago by
thomas.heigl.ibk
• 0
1
vote
1
reply
192
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 3 days ago by
SamGG
▴ 330 • written 5 weeks ago by
jarod
▴ 30
1
vote
2
replies
141
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
199
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 3 days ago by
alan.ocallaghan
▴ 150 • written 5 days ago by
Najla Abassi
• 0
1
vote
8
replies
286
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
Amit
• 0
1
vote
3
replies
189
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 1 day ago by
mercedeh.movassagh
▴ 10 • written 9 days ago by
María
• 0
1
vote
2
replies
117
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
3 days ago • updated 2 days ago
Mj.A.
• 0
0
votes
0
replies
25
views
Materials for liposomes
alabaster.schemas
metaMSdata
1 day ago
bocsciences
• 0
0
votes
0
replies
24
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
1 day ago
Pierre Lindenbaum
▴ 10
0
votes
2
replies
1.0k
views
error when using M-values in ChAMP
ChAMP
updated 1 day ago by
hortenseguillaume96
• 0 • written 6.2 years ago by
a.mcneill
• 0
0
votes
1
reply
57
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
updated 23 hours ago by
James W. MacDonald
65k • written 23 hours ago by
w.cookson
• 0
0
votes
1
reply
43
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 17 hours ago by
Michael Love
41k • written 18 hours ago by
Mikushi
• 0
0
votes
1
reply
58
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 3 hours ago by
Gordon Smyth
50k • written 17 hours ago by
Fabian
• 0
0
votes
3
replies
79
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 2 hours ago by
Michael Love
41k • written 18 hours ago by
Faisal
• 0
0
votes
0
replies
13
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
2 hours ago
Ankit
▴ 20
0
votes
0
replies
9
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
2 hours ago
feather-W
• 0
0
votes
6
replies
146
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
3 days ago • updated 1 hour ago
Jitendra
▴ 10
0
votes
0
replies
71
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
6 days ago
Maria Doyle
▴ 70
0
votes
3
replies
37
views
fgsea fork
fgsea
updated 11 minutes ago by
shepherl
3.8k • written 11 hours ago by
yimjohns
• 0
0
votes
3
replies
2.2k
views
internal error in trio library when trying to use lfmm() in LEA package
lfmm
LEA
updated 4 days ago by
m.charters
• 0 • written 2.9 years ago by
valentinarov
• 0
0
votes
1
reply
204
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
updated 4 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
Gordon
• 0
0
votes
0
replies
48
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
4 days ago
gshweta95
• 0
0
votes
1
reply
560
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
written 9 months ago by
abhisek001
• 0
0
votes
2
replies
525
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 4 days ago by
CHEN
• 0 • written 10 months ago by
Saanchi
• 0
0
votes
2
replies
100
views
bioconductor emailing list
Bioconductor
updated 3 days ago by
shepherl
3.8k • written 4 days ago by
1427972815
• 0
0
votes
6
replies
328
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
22 days ago • updated 3 days ago
Lily Cheang
• 0
0
votes
1
reply
90
views
collapseReplicates dimension error
DESeq2
Dese
updated 3 days ago by
Michael Love
41k • written 7 days ago by
Léa
• 0
0
votes
4
replies
306
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
11 days ago • updated 3 days ago
Efra
• 0
0
votes
2
replies
104
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 3 days ago by
Michael Love
41k • written 3 days ago by
SG
• 0
0
votes
1
reply
147
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
24 days ago • updated 3 days ago
shepherl
3.8k
0
votes
7
replies
343
views
DESeq2 filtering vs edgeR filtering
DESeq2
16 days ago • updated 2 days ago
fr8712ca-s
• 0
0
votes
1
reply
139
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 2 days ago by
Guido Hooiveld
★ 3.9k • written 10 days ago by
Julie
• 0
0
votes
3
replies
168
views
PCA of different bacterial species
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Laura
▴ 10
0
votes
1
reply
43
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
Karen
• 0
43 results • Page
1 of 1
Recent ...
Replies
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Awards
• All
Popular Question
to
Dario Strbenac
★ 1.5k
Popular Question
to
Ankit
▴ 20
Popular Question
to
michael.s
• 0
Popular Question
to
James W. MacDonald
65k
Popular Question
to
Pierre Lindenbaum
▴ 10
Locations
• All
Switzerland,
3 minutes ago
United States,
6 minutes ago
St Louis, MO,
8 minutes ago
United Kingdom,
11 minutes ago
France/Marseille/Inserm,
21 minutes ago
Traffic: 787 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