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2
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2
replies
1.4k
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DESeq2 on multilevel design variable
DESeq2
updated 2.5 years ago by
swbarnes2
★ 1.4k • written 2.5 years ago by
Amdom
• 0
0
votes
1
reply
808
views
Generate false reads for testing
mgu74bv2cdf
Software
Alignment
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
Franck RICHARD
• 0
0
votes
1
reply
1.1k
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 2.5 years ago by
Michael Love
43k • written 2.6 years ago by
Fred
• 0
0
votes
1
reply
795
views
BiocManager Package installs
Bioconductor
updated 2.5 years ago by
shepherl
4.2k • written 2.6 years ago by
joseph.cerra
• 0
0
votes
3
replies
1.3k
views
Extract Limma Adjusted Values for Plotting
limma
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
phelankj
▴ 10
0
votes
0
replies
841
views
plotGOTermGraph connects all subtrees to the root node
GO.db
GOstats
2.6 years ago
RuBBiT0
▴ 10
0
votes
2
replies
1.6k
views
News:
List of Deprecated Packages for Bioc3.17
Bioconductor
Deprecation
Devel
devel
2.7 years ago • updated 2.6 years ago
shepherl
4.2k
8
votes
13
replies
3.5k
views
Interpret plot from DiffBind
DiffBind
updated 2.5 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
Chris
▴ 20
0
votes
2
replies
2.3k
views
Handling NA's in Deseq2
Dese
DESeq2
2.6 years ago • updated 2.5 years ago
Asger Mølgaard
• 0
0
votes
0
replies
1.0k
views
Positive beta-scores of essential genes in drug-treated cells
mageck
MAGeCKFlute
CrisprScreen
2.6 years ago
Monika
• 0
2
votes
4
replies
1.9k
views
Use with_go along with other filters in getBM function
Annotation
biomaRt
2.6 years ago
RuBBiT0
▴ 10
0
votes
2
replies
1.3k
views
Remove duplicate genera in DEseq output?
DESeq2
updated 2.6 years ago by
Lluís Revilla Sancho
▴ 760 • written 2.6 years ago by
Bretta
• 0
0
votes
2
replies
1.5k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
2.6 years ago
dwas
• 0
3
votes
6
replies
1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
553
views
alpha1 in SAFFRON method in onlineFDR package
onlineFDR
2.6 years ago
lgomeso
• 0
0
votes
0
replies
662
views
Title in dba.plotProfile
DiffBind
2.6 years ago
agata17
• 0
0
votes
2
replies
1.6k
views
Proteomics data with NA values
Proteomics
ProteoMM
ProteomicsWorkflow
updated 2.4 years ago by
mmvar
• 0 • written 2.6 years ago by
nkvnambiar
• 0
0
votes
2
replies
2.0k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 2.6 years ago by
hfbarrerat
• 0 • written 4.8 years ago by
Bethan
• 0
2
votes
4
replies
1.2k
views
BiocGenerics binary is outdated for macOS ARM
BiocGenerics
2.6 years ago
Michael Steinbaugh
▴ 90
0
votes
3
replies
1.2k
views
Multitasking and Rbwa
Rbwa
Alignment
written 2.6 years ago by
Franck RICHARD
• 0
0
votes
0
replies
660
views
News:
May 31st is the last day to nominate for Bioc2023 Awards!
Bioconductor
Awards
Bioc2023
Recognition
2.6 years ago
shepherl
4.2k
0
votes
6
replies
1.5k
views
Merge 2 accounts, or delete 1 account.
Bioconductor
ALL
2.6 years ago • updated 2.5 years ago
simone.tiberi
• 0
0
votes
0
replies
2.1k
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
2.6 years ago
pg45863
▴ 10
1
vote
2
replies
1.0k
views
Normalized counts from LRT or Wald test?
DESeq2
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
sneha108ss
• 0
2
votes
1
reply
900
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR
DESeq2
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
calvincornell1996
• 0
0
votes
0
replies
724
views
Error while performing DEXseq
DEXSeq
2.6 years ago
vipul14
• 0
1
vote
2
replies
1.0k
views
Extracting fitted expression matrix from Limma
limma
2.6 years ago
sarah.kelliher
• 0
5
votes
11
replies
7.5k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 2.6 years ago by
Sabiha
▴ 20
0
votes
0
replies
611
views
Subsite info is possible for more studies
curatedMetagenomicData
2.6 years ago
Vitor Heidrich
• 0
3
votes
11
replies
4.9k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
2.6 years ago • updated 2.5 years ago
Anna
▴ 20
0
votes
0
replies
868
views
News:
Reminder: BioC2023, Awards, TAB Deadline approaching - May 31st!
Bioconductor
Community
BioC2023
2.6 years ago
Maria Doyle
▴ 110
5
votes
7
replies
2.3k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
1.0k
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 2.5 years ago by
Michael Love
43k • written 2.6 years ago by
suphamon.j
▴ 20
0
votes
1
reply
907
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
littlefishes20
▴ 10
0
votes
1
reply
1.2k
views
DiffBind dba() in parallel
DiffBind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
Shashank
• 0
1
vote
4
replies
2.3k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
lin.pei26
• 0
3
votes
5
replies
2.9k
views
Error: 'IdClusters'
DECIPHER
updated 2.6 years ago by
Ling-Hsiu
▴ 10 • written 2.9 years ago by
julieta.micorriza
• 0
2
votes
1
reply
1.1k
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 2.6 years ago by
andres.firrincieli
▴ 50 • written 2.6 years ago by
hesse.sebastian
▴ 10
2
votes
4
replies
3.3k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot
clusterProfiler
2.6 years ago
Tyroone
• 0
0
votes
1
reply
857
views
HiCDCPlus glm.fit error
HiCDCPlus
updated 2.5 years ago by
merve.sahn
• 0 • written 2.6 years ago by
ehamrud
• 0
0
votes
2
replies
1.3k
views
DoparParam() execution fails when foreach() works
clustermq
doparallel
DESeq2
2.6 years ago
boris
• 0
2
votes
6
replies
1.9k
views
How to update a package at Bioconductor
diffGeneAnalysis
DifferentialExpression
updated 2.5 years ago by
shepherl
4.2k • written 2.6 years ago by
ma79
• 0
0
votes
0
replies
818
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
2.6 years ago
Levi
• 0
1
vote
0
replies
1.0k
views
Fold values in Diffbind
DiffBind
2.6 years ago
bhandary.8590
▴ 20
1
vote
2
replies
1.6k
views
Error: biomaRt has encountered an unexpected server error.
biomaRt
updated 2.6 years ago by
Mike Smith
★ 6.6k • written 2.6 years ago by
Yijing
• 0
0
votes
0
replies
1.0k
views
Illumina global SNP screeing array
illuminaHumanv3.db
arrays
2.6 years ago
DH
• 0
2
votes
3
replies
1.3k
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 2.6 years ago by
jandrade
• 0
1
vote
4
replies
1.4k
views
Submitting BSgenome package for a new assembly
bsgenome
GenomicFeatures
package
updated 2.6 years ago by
Hervé Pagès
16k • written 2.6 years ago by
Manish
• 0
0
votes
2
replies
1.8k
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2
NanoStringDiff
limma
2.6 years ago
pg45863
▴ 10
0
votes
1
reply
1.0k
views
how to solve this error
DESeq2
GEO
miRNAData
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
ashisaanz
• 0
46,699 results • Page
51 of 934
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Replies
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.…
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 …
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
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