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
4
replies
1.5k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
20 months ago
Lucy
▴ 60
0
votes
1
reply
669
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Leyre
• 0
0
votes
2
replies
1.1k
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
20 months ago
Seongsu
• 0
0
votes
2
replies
902
views
Gene Ontology doubt
microbiomeExplorer
20 months ago
Bhawna
• 0
0
votes
1
reply
838
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 20 months ago by
Michael Love
43k • written 21 months ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
958
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
ja569116
• 0
0
votes
2
replies
846
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
20 months ago
fer_talavera
• 0
0
votes
7
replies
2.3k
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
20 months ago
needNGS
• 0
15
votes
23
replies
5.4k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
21 months ago • updated 19 months ago
Chris
▴ 20
3
votes
6
replies
2.3k
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
written 21 months ago by
Fabian
• 0
0
votes
4
replies
1.1k
views
Minfi - estimatecellscount
min
minfi
updated 19 months ago by
James W. MacDonald
68k • written 21 months ago by
clacarion
• 0
0
votes
0
replies
656
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
21 months ago
feather-W
• 0
0
votes
0
replies
645
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
21 months ago
Ankit
▴ 20
0
votes
6
replies
1.3k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Faisal
• 0
1
vote
5
replies
1.2k
views
fgsea fork
fgsea
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
yimjohns
• 0
0
votes
1
reply
449
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Mikushi
• 0
0
votes
0
replies
632
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
21 months ago
Pierre Lindenbaum
▴ 10
2
votes
8
replies
1.4k
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Amit
• 0
0
votes
1
reply
702
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Karen
• 0
2
votes
4
replies
1.4k
views
PCA of different bacterial species
DESeq2
written 21 months ago by
Laura
▴ 10
1
vote
2
replies
780
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
21 months ago
Mj.A.
▴ 20
0
votes
1
reply
1.7k
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
21 months ago
shepherl
4.2k
0
votes
2
replies
1.1k
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 21 months ago by
Michael Love
43k • written 21 months ago by
SG
• 0
2
votes
3
replies
1.1k
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 21 months ago by
Wei Shi
★ 3.6k • written 21 months ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
2.3k
views
From a DNAStringSet to a data.frame
Biostrings
21 months ago
ramiro.barrantes
▴ 10
0
votes
1
reply
613
views
collapseReplicates dimension error
DESeq2
Dese
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Léa
• 0
5
votes
25
replies
3.2k
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 20 months ago by
Gordon Smyth
53k • written 21 months ago by
Jitendra
▴ 10
2
votes
4
replies
903
views
bioconductor emailing list
Bioconductor
21 months ago • updated 16 months ago
XFWu
• 0
3
votes
2
replies
801
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
21 months ago
Anita
▴ 10
3
votes
3
replies
2.4k
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 21 months ago by
alan.ocallaghan
▴ 160 • written 21 months ago by
Najla Abassi
• 0
2
votes
1
reply
1.0k
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Dario Strbenac
★ 1.6k
0
votes
0
replies
802
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
21 months ago
gshweta95
• 0
0
votes
2
replies
2.0k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
21 months ago • updated 20 months ago
Gordon
• 0
7
votes
6
replies
1.3k
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Amit
• 0
2
votes
2
replies
1.5k
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
written 21 months ago by
enee
▴ 10
0
votes
1
reply
1.2k
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
updated 6 months ago by
Ray
• 0 • written 21 months ago by
Maria Doyle
▴ 110
0
votes
1
reply
1.1k
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
scoops_streams_06
• 0
0
votes
0
replies
493
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
21 months ago
nromerov
• 0
1
vote
2
replies
899
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
21 months ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
829
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 21 months ago by
Marcel Ramos
700 • written 21 months ago by
Astrid Deschênes
• 0
8
votes
5
replies
3.4k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 13 months ago by
Gordon Smyth
53k • written 21 months ago by
Jack S.
▴ 60
4
votes
4
replies
5.3k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 21 months ago by
jandrade
• 0 • written 8.0 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
2
replies
2.0k
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
21 months ago
kcarey
• 0
0
votes
0
replies
713
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
21 months ago
mayra.haedo
• 0
0
votes
0
replies
593
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
21 months ago
erbrocato
• 0
1
vote
4
replies
1.2k
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
21 months ago
samuel.channon
• 0
2
votes
3
replies
862
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
andrebolerbarros
▴ 20
0
votes
3
replies
962
views
Help with Complex DESeq2 Design
DESeq2
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
kelsey.beavers
• 0
0
votes
1
reply
773
views
Visium RNA
metaMSdata
written 21 months ago by
Karlison
• 0
1
vote
2
replies
1.3k
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
maximilian.beikirch
• 0
46,699 results • Page
28 of 934
Recent ...
Replies
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
aqeel
• 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
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.…
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
Istvan Albert
▴ 50
Popular Question
to
Dario Strbenac
★ 1.6k
Scholar
to
Nikos Ignatiadis
▴ 180
Popular Question
to
Robert
• 0
Popular Question
to
lamia11me
• 0
Locations
• All
The city by the bay,
7 minutes ago
Pakistan,
9 minutes ago
WEHI, Melbourne, Australia,
1 hour ago
United States,
3 hours ago
Brazil,
3 hours ago
Traffic: 953 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