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0
votes
2
replies
774
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Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings
aminoacid
motifbreakR
written 15 months ago by
wilson_ava
• 0
1
vote
2
replies
810
views
Student
metaboliteIDmapping
Metabolomics
KEGG
updated 14 months ago by
deeenes
▴ 60 • written 14 months ago by
vipinsapla
• 0
2
votes
5
replies
1.2k
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes
ATACSeq
14 months ago
ronin
• 0
0
votes
13
replies
2.1k
views
When doing differential methylation using the sesame package, seems to only go one way
methylation
sesame
methylationArrayAnalysis
updated 14 months ago by
zhouwanding
▴ 20 • written 14 months ago by
ramiro.barrantes
▴ 10
17
votes
9
replies
8.3k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 14 months ago by
James W. MacDonald
68k • written 9.5 years ago by
ompandey
▴ 10
0
votes
0
replies
510
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
14 months ago
Alejandro
• 0
0
votes
0
replies
892
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel
scran
BiocParall
14 months ago
Lluís Revilla Sancho
▴ 760
2
votes
2
replies
808
views
How to read OSCA book?
BIOCON
OSCA
Bioconductor
14 months ago
zr
• 0
0
votes
1
reply
607
views
Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome
DESeq2
updated 14 months ago by
Michael Love
43k • written 14 months ago by
eric
• 0
0
votes
1
reply
642
views
QSEA:Error in h(simpleError(msg, call))
qsea
14 months ago
kf
• 0
2
votes
1
reply
742
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray
EpigeneticsWorkflow
limma
Regression
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
rae.alshammari
▴ 20
7
votes
9
replies
2.0k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO
clusterProfiler
enr
updated 14 months ago by
Guido Hooiveld
★ 4.1k • written 14 months ago by
Fatima
• 0
0
votes
0
replies
636
views
Mark seleced variables in the x-loading plot
OPLS
genomes
Proteomics
14 months ago
Ragnhild
• 0
0
votes
0
replies
704
views
News:
Metabolomics with R/Bioconductor Online Course
metabomxtr
MetaboCoreUtils
metabolomicsWorkbenchR
Metabolomics
14 months ago
info
▴ 10
2
votes
1
reply
585
views
object 'hdac_targets' not found
TPP
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Alexandre Mahé
• 0
1
vote
2
replies
844
views
KEGGgraph result difference
igraph
KEGGgraph
RCy3
GraphNEL
14 months ago • updated 13 months ago
Arindam
▴ 80
0
votes
1
reply
1.4k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings
packageinstallation
updated 14 months ago by
Aidan
▴ 70 • written 14 months ago by
semra
• 0
1
vote
2
replies
1.1k
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray
methylation
sesame
methylationArrayAnalysis
15 months ago • updated 14 months ago
ramiro.barrantes
▴ 10
0
votes
1
reply
630
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 14 months ago by
Lluís Revilla Sancho
▴ 760 • written 14 months ago by
emilymily77
• 0
1
vote
2
replies
787
views
WARNING: No Bioconductor dependencies detected.
Bioconductor
Biocon
15 months ago • updated 14 months ago
katja.danielzik
• 0
0
votes
5
replies
1.2k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 14 months ago by
Yang Liao
▴ 450 • written 15 months ago by
venusian.martin
• 0
0
votes
1
reply
703
views
Annotating DMRs
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
ramiro.barrantes
▴ 10
0
votes
2
replies
812
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 15 months ago by
swbarnes2
★ 1.4k • written 15 months ago by
Megan
• 0
0
votes
3
replies
857
views
concentration tables suitable as input for new packages?
Bioconductor
written 15 months ago by
katja.danielzik
• 0
2
votes
0
replies
1.0k
views
News:
Save the Date for EuroBioC2025 in Barcelona!
EuroBioC2025
Conference
Bioconductor
Community
15 months ago
Maria Doyle
▴ 110
0
votes
1
reply
657
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
bioinformaticssrm2011
• 0
0
votes
5
replies
2.3k
views
DESeq2 Multi-factor design not full rank
RNASeq
DESeq2
written 4.6 years ago by
jehimi
• 0
0
votes
5
replies
1.5k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor
clusterProfiler
updated 14 months ago by
Lluís Revilla Sancho
▴ 760 • written 15 months ago by
semra
• 0
0
votes
0
replies
732
views
Job:
Postdoctoral Research Associate in Computational Epigenomics
Phd
SingleCell
DNAMethylation
Shanghai
JobPosting
15 months ago
xiaolong
• 0
0
votes
1
reply
621
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 15 months ago by
Vincent J. Carey, Jr.
6.7k • written 15 months ago by
kmzhou4
• 0
1
vote
1
reply
866
views
Help with design matrix for RNA-seq data using edgeR
edgeR
RNASeqData
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
erik.burchard
• 0
3
votes
6
replies
2.0k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
micolak0115
• 0
0
votes
2
replies
736
views
tximport data import
tximport
updated 15 months ago by
Michael Love
43k • written 15 months ago by
rodongo
• 0
2
votes
2
replies
854
views
Should tSNE from biol. replicates look alike?
scRNAseq
SingleCellExperiment
batchelor
written 15 months ago by
Jose Guillen
▴ 10
0
votes
0
replies
688
views
Problem merging metadata and feature-table before analysing LEfSe on R
microbiomeDataSets
differential-abundance
15 months ago
샤니쿠마리
• 0
2
votes
2
replies
1.2k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
15 months ago
Assa Yeroslaviz
★ 1.5k
1
vote
2
replies
3.1k
views
How to use compareCluster in ClusterProfiler?
RNASeqData
GSEA
clusterProfiler
written 15 months ago by
b8177
• 0
0
votes
4
replies
2.1k
views
News:
Announcing GBCC 2025: The first-ever joint conference between Bioconductor and Galaxy!
Conference
Bioconductor
Community
updated 7 weeks ago by
dzv20413
• 0 • written 15 months ago by
Maria Doyle
▴ 110
0
votes
1
reply
2.1k
views
Unable to install/use limma
limma
Bioconductor
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Jennifer
• 0
1
vote
3
replies
1.8k
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 15 months ago by
James W. MacDonald
68k • written 22 months ago by
Pez
▴ 10
1
vote
1
reply
808
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray
ChAMP
R
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Fateme
• 0
0
votes
2
replies
724
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion
ReactomeGSA
BatchEffect
written 15 months ago by
Shaimaa Gamal
• 0
3
votes
6
replies
32k
views
Deseq: What does "BaseMean" mean?
deseq2
written 7.2 years ago by
183227851
• 0
0
votes
1
reply
1.4k
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 15 months ago by
Guido Hooiveld
★ 4.1k • written 15 months ago by
sherinesaber
• 0
0
votes
0
replies
490
views
Z-score Interpretation across components
MAST
15 months ago
GJ
• 0
0
votes
1
reply
577
views
error for the geneGOEnricher function of the NoRCE package
NoRCE
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Luca
• 0
0
votes
2
replies
1.6k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq
DESeq2
updated 15 months ago by
swbarnes2
★ 1.4k • written 15 months ago by
Shwetal
• 0
1
vote
4
replies
1.8k
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN
biomaRt
updated 13 months ago by
Adam
• 0 • written 15 months ago by
varga.luca
• 0
1
vote
5
replies
2.2k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler
heatmaps
written 15 months ago by
Claudio
• 0
1
vote
2
replies
668
views
Review process for delivering R packages
Bioconductor
15 months ago
XFWu
• 0
46,691 results • Page
16 of 934
Recent ...
Replies
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…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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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