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
6
replies
2.3k
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
2.1 years ago
erika.maldonado-rosado
• 0
1
vote
2
replies
1.3k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 2.1 years ago by
meenae
▴ 10
0
votes
2
replies
1.0k
views
How can I devise a method like DESeq2 to give statistics for paired multiple -omic datasets?
DESeq2
updated 2.1 years ago by
edammer
• 0 • written 2.1 years ago by
Christina
• 0
0
votes
0
replies
663
views
proActiv - Error in estimateSizeFactorsForMatrix when using the proActiv function
proActiv
error
estimateSizeFactorsForMatrix
2.1 years ago
Chris
• 0
0
votes
5
replies
1.3k
views
error while running DMRcate
stattistics
epicarray
Epigenetics
DMRcate
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
Jitendra
▴ 10
0
votes
4
replies
1.4k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 20 months ago by
Michael Love
43k • written 2.1 years ago by
Crystal571
• 0
0
votes
1
reply
1.2k
views
DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
DMRcate
DMR.plot
updated 2.1 years ago by
shepherl
4.2k • written 2.1 years ago by
Chiara
• 0
0
votes
1
reply
1.5k
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
2.1 years ago
leon
• 0
0
votes
5
replies
1.4k
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 2.0 years ago by
Gordon Smyth
53k • written 2.2 years ago by
e.vanzanten.1
• 0
0
votes
1
reply
634
views
MEDIPS - covariate
MEDIPS
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
James
• 0
0
votes
1
reply
1.4k
views
Job:
Job:Data Scientist / Bioinformatician / Statistician at University of California San Francisco (UCSF)
programming
datascientist
psychiatry
bioinformatics
JobPosting
2.2 years ago • updated 2.1 years ago
Belinda
• 0
2
votes
3
replies
2.7k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 2.1 years ago by
swbarnes2
★ 1.4k • written 2.2 years ago by
Sam
• 0
2
votes
4
replies
1.5k
views
Need help generating BSgenome and orgdb
OrgDb
BSgenome
2.2 years ago • updated 22 months ago
mat149
▴ 80
1
vote
1
reply
1.2k
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 2.2 years ago by
Hervé Pagès
16k • written 2.2 years ago by
Anna
▴ 10
1
vote
3
replies
1.4k
views
Using injectSNPs with a custom set of SNPs
SNPlocs
BSgenome
written 2.2 years ago by
Stevie Pederson
• 0
6
votes
7
replies
1.8k
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
jonas.freimuth
▴ 20
0
votes
0
replies
754
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
2.2 years ago
Sara
• 0
0
votes
2
replies
769
views
DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
DESeq2
2.2 years ago • updated 2.1 years ago
Roey Angel
• 0
0
votes
4
replies
1.6k
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO
ensembldb
2.2 years ago
Rockbar
• 0
2
votes
4
replies
1.5k
views
Question about creating custom organism database with AnnotationForge
AnnotationForge
2.2 years ago
Adrian
• 0
0
votes
0
replies
851
views
News:
COURSE - Developing R/Bioconductor Packages for Genomics
Bioconductor
PackageTypeData
PackageType
2.2 years ago
info
▴ 10
0
votes
2
replies
1.1k
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
2.2 years ago
Karthik
• 0
0
votes
1
reply
1.9k
views
DESeq2 Error in Results Contrast and ResultsNames
DESeq2
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
J_Can
• 0
0
votes
2
replies
1.3k
views
recount3 monorail pipeline version
recount3
2.2 years ago • updated 24 months ago
Lorenzo
• 0
2
votes
0
replies
578
views
bioNeuro plot_expression_profile - how to order samples in plot output
plot_expression_profile
BioNERO
2.2 years ago
Christopher
▴ 20
0
votes
0
replies
745
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
2.2 years ago
Florian
• 0
0
votes
1
reply
2.3k
views
choosing rank for GSEA
gsea
DESeq2
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Grace.Ciabattoni
• 0
0
votes
0
replies
1.0k
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
2.2 years ago
Xinqi
• 0
1
vote
2
replies
1.5k
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta
AnnotationHub
AnnotationHubData
2.2 years ago
Thon
• 0
0
votes
0
replies
898
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
2.2 years ago
Sara
• 0
1
vote
5
replies
1.2k
views
Duplicated expression values?
depmap_copyNumber()
depmap
written 2.2 years ago by
davi.vuko
• 0
2
votes
2
replies
918
views
"Details" section for specific software packages
Website
updated 2.2 years ago by
Mike Smith
★ 6.6k • written 2.2 years ago by
Justin
• 0
0
votes
1
reply
2.7k
views
edgeR heatmap construction and interpretation
heatmaps
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
ulin.1
• 0
1
vote
2
replies
870
views
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
2.2 years ago
Benji Bromberg
▴ 30
1
vote
1
reply
1.1k
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
fuqichen1
• 0
0
votes
3
replies
1.3k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon
tximport
deseq2
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
Kayleigh
• 0
3
votes
6
replies
2.5k
views
Subsetting Range Summarized Experiment
SummarizedExperiment
2.2 years ago
Bine
▴ 50
0
votes
0
replies
726
views
How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS
admixMap
2.2 years ago
mailtoshivam13
• 0
0
votes
2
replies
1.9k
views
Using dplyr commands with DataFrame objects
S4Vectors
2.2 years ago
GE
• 0
0
votes
4
replies
2.1k
views
News:
Important Bioconductor Release 3.18 deadlines this week
Release
Devel
release
devel
updated 2.2 years ago by
Guido Hooiveld
★ 4.1k • written 2.2 years ago by
shepherl
4.2k
0
votes
2
replies
1.5k
views
enrichPlot error when plotting topGO results
topGO
enrichplot
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
nromerov
• 0
0
votes
1
reply
1.2k
views
GenomeInfoDbData version 1.2.9
GenomeInfoDbData
updated 2.2 years ago by
shepherl
4.2k • written 2.2 years ago by
remi.trimbour
• 0
0
votes
5
replies
1.8k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi
limma
2.2 years ago
dorota.komar
• 0
2
votes
5
replies
1.9k
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge
makeOrgPackageFromNCBI
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
mat149
▴ 80
2
votes
2
replies
2.2k
views
Long-read mode in featureCounts
Rsubread
LongRead
2.2 years ago
mmisak
• 0
0
votes
1
reply
845
views
Issue with weights in voomLmFit()
limma
updated 13 months ago by
Gordon Smyth
53k • written 2.2 years ago by
gabriel.hoffman
▴ 170
0
votes
2
replies
1.5k
views
minfi differential methylation analysis errors
minfi
2.2 years ago
matthew.sinton
• 0
1
vote
2
replies
1.2k
views
tximeta error with vroom
tximeta
vroom
2.2 years ago
Pufall, Miles A
▴ 30
2
votes
4
replies
2.4k
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19
AnnotationDbi
2.2 years ago
Erica
• 0
0
votes
1
reply
1.2k
views
Multiple groups comparison using Linnorm
Linnorm
DEG
MultipleComparison
updated 2.2 years ago by
shunyip
• 0 • written 4.4 years ago by
awakumaya
• 0
46,695 results • Page
40 of 934
Recent ...
Replies
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards
• All
Popular Question
to
lamia11me
• 0
Popular Question
to
Gordon Smyth
53k
Popular Question
to
Michael Love
43k
Popular Question
to
Luca
• 0
Popular Question
to
Lluís Revilla Sancho
▴ 760
Locations
• All
WEHI, Melbourne, Australia,
1 hour ago
United States,
2 hours ago
United States,
3 hours ago
United States,
4 hours ago
United States,
4 hours ago
Traffic: 899 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