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Harmonizing RNA-seq data of different sourceS(cell vs. tissue) to further conduct unsupervised clustering analysis?
HarmonizedTCGAData
21 minutes ago
bioinformata
• 0
0
votes
0
replies
13
views
DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2
Bioconductor
2 hours ago
JT
• 0
0
votes
0
replies
15
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
6 hours ago
Alejandro
• 0
0
votes
0
replies
17
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel
scran
BiocParall
7 hours ago
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
86
views
How to read OSCA book?
BIOCON
OSCA
Bioconductor
updated 7 hours ago by
Lluís Revilla Sancho
▴ 730 • written 2 days ago by
zr
• 0
0
votes
1
reply
63
views
Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome
DESeq2
updated 1 day ago by
Michael Love
42k • written 1 day ago by
eric
• 0
0
votes
1
reply
96
views
QSEA:Error in h(simpleError(msg, call))
qsea
2 days ago
kf
• 0
2
votes
1
reply
105
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray
EpigeneticsWorkflow
limma
Regression
updated 3 days ago by
James W. MacDonald
67k • written 3 days ago by
rae.alshammari
▴ 10
2
votes
8
replies
673
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO
clusterProfiler
enr
updated 1 hour ago by
James W. MacDonald
67k • written 3 days ago by
Fatima
• 0
0
votes
12
replies
378
views
When doing differential methylation using the sesame package, seems to only go one way
methylation
sesame
methylationArrayAnalysis
updated 3 hours ago by
James W. MacDonald
67k • written 3 days ago by
ramiro.barrantes
▴ 10
0
votes
0
replies
76
views
Mark seleced variables in the x-loading plot
OPLS
genomes
Proteomics
3 days ago
Ragnhild
• 0
0
votes
0
replies
63
views
News:
Metabolomics with R/Bioconductor Online Course
metabomxtr
MetaboCoreUtils
metabolomicsWorkbenchR
Metabolomics
3 days ago
info
▴ 10
2
votes
1
reply
116
views
object 'hdac_targets' not found
TPP
updated 3 days ago by
James W. MacDonald
67k • written 4 days ago by
Alexandre Mahé
• 0
0
votes
1
reply
98
views
KEGGgraph result difference
igraph
KEGGgraph
RCy3
GraphNEL
updated 4 days ago by
alex.pico
▴ 20 • written 4 days ago by
Arindam
▴ 80
0
votes
0
replies
67
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings
packageinstallation
4 days ago
semra
• 0
1
vote
2
replies
211
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray
methylation
sesame
methylationArrayAnalysis
4 days ago • updated 3 days ago
ramiro.barrantes
▴ 10
0
votes
1
reply
96
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 4 days ago by
Lluís Revilla Sancho
▴ 730 • written 4 days ago by
emilymily77
• 0
1
vote
2
replies
153
views
WARNING: No Bioconductor dependencies detected.
Bioconductor
Biocon
5 days ago • updated 4 days ago
katja.danielzik
• 0
0
votes
3
replies
238
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 3 days ago by
Yang Liao
▴ 440 • written 5 days ago by
venusian.martin
• 0
0
votes
1
reply
100
views
Annotating DMRs
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 5 days ago by
James W. MacDonald
67k • written 5 days ago by
ramiro.barrantes
▴ 10
0
votes
2
replies
302
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 6 days ago by
swbarnes2
★ 1.4k • written 12 days ago by
Megan
• 0
0
votes
2
replies
203
views
concentration tables suitable as input for new packages?
Bioconductor
7 days ago • updated 6 days ago
katja.danielzik
• 0
2
votes
0
replies
154
views
News:
Save the Date for EuroBioC2025 in Barcelona!
EuroBioC2025
Conference
Bioconductor
Community
7 days ago
Maria Doyle
▴ 90
0
votes
1
reply
111
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 5 days ago by
James W. MacDonald
67k • written 7 days ago by
bioinformaticssrm2011
• 0
0
votes
5
replies
1.5k
views
DESeq2 Multi-factor design not full rank
RNASeq
DESeq2
written 3.3 years ago by
jehimi
• 0
0
votes
4
replies
288
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor
clusterProfiler
updated 6 days ago by
James W. MacDonald
67k • written 7 days ago by
semra
• 0
0
votes
0
replies
129
views
Job:
Postdoctoral Research Associate in Computational Epigenomics
Phd
SingleCell
DNAMethylation
Shanghai
JobPosting
9 days ago
xiaolong
• 0
0
votes
1
reply
170
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 9 days ago by
Vincent J. Carey, Jr.
6.7k • written 9 days ago by
kmzhou4
• 0
0
votes
0
replies
147
views
News:
Bioconductor 3.20 Release Schedule
software
release
Release
10 days ago
shepherl
4.0k
1
vote
1
reply
256
views
Help with design matrix for RNA-seq data using edgeR
edgeR
RNASeqData
updated 10 days ago by
Gordon Smyth
51k • written 12 days ago by
erik.burchard
• 0
3
votes
6
replies
1.2k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 8 days ago by
Michael Love
42k • written 11 days ago by
micolak0115
• 0
0
votes
2
replies
262
views
tximport data import
tximport
updated 11 days ago by
Michael Love
42k • written 11 days ago by
rodongo
• 0
2
votes
1
reply
182
views
Should tSNE from biol. replicates look alike?
scRNAseq
SingleCellExperiment
batchelor
updated 11 days ago by
James W. MacDonald
67k • written 11 days ago by
Jose Guillen
▴ 10
0
votes
0
replies
124
views
Problem merging metadata and feature-table before analysing LEfSe on R
microbiomeDataSets
differential-abundance
11 days ago
샤니쿠마리
• 0
2
votes
2
replies
477
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
12 days ago • updated 11 days ago
Assa Yeroslaviz
★ 1.5k
1
vote
1
reply
263
views
How to use compareCluster in ClusterProfiler?
RNASeqData
GSEA
clusterProfiler
updated 12 days ago by
Guido Hooiveld
★ 4.1k • written 12 days ago by
b8177
• 0
0
votes
0
replies
148
views
News:
Announcing GBCC 2025: The first-ever joint conference between Bioconductor and Galaxy!
Conference
Bioconductor
Community
13 days ago
Maria Doyle
▴ 90
0
votes
1
reply
176
views
Unable to install/use limma
limma
Bioconductor
updated 13 days ago by
James W. MacDonald
67k • written 13 days ago by
Jennifer
• 0
1
vote
3
replies
581
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 13 days ago by
James W. MacDonald
67k • written 7 months ago by
Pez
▴ 10
1
vote
1
reply
246
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray
ChAMP
R
updated 13 days ago by
James W. MacDonald
67k • written 15 days ago by
Fateme
• 0
0
votes
1
reply
188
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion
ReactomeGSA
BatchEffect
updated 11 days ago by
jg
▴ 20 • written 14 days ago by
Shaimaa Gamal
• 0
3
votes
6
replies
25k
views
Deseq: What does "BaseMean" mean?
deseq2
written 6.0 years ago by
183227851
• 0
0
votes
1
reply
299
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 14 days ago by
Guido Hooiveld
★ 4.1k • written 16 days ago by
sherinesaber
• 0
0
votes
0
replies
229
views
Z-score Interpretation across components
MAST
16 days ago
Greg
• 0
0
votes
1
reply
253
views
error for the geneGOEnricher function of the NoRCE package
NoRCE
updated 16 days ago by
James W. MacDonald
67k • written 17 days ago by
Luca
• 0
0
votes
2
replies
685
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq
DESeq2
updated 17 days ago by
swbarnes2
★ 1.4k • written 17 days ago by
Shwetal
• 0
1
vote
2
replies
276
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN
biomaRt
17 days ago • updated 14 days ago
varga.luca
• 0
1
vote
5
replies
558
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler
heatmaps
written 29 days ago by
Claudio
• 0
1
vote
2
replies
264
views
Review process for delivering R packages
Bioconductor
18 days ago
XFWu
• 0
4
votes
11
replies
596
views
Size factor normalized counts for between sample comparisons - correct?
DESeq2
19 days ago • updated 17 days ago
boczniak767
▴ 740
46,009 results • Page
1 of 921
Recent ...
Replies
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
by
James W. MacDonald
67k
Hi Guido, It's that last filtering step. You are saying the NCBI Gene ID has to be unique AND the ontology has to be BP, which isn't what …
Comment: AffylmGUI does not start wit R 4.4.1
by
richardallenfriedmanbrooklyn
▴ 20
Gordon, I found out what went wrong. The problem was that the xquartz distribution for mac from cran did not include tcltk! I found that b…
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
by
Guido Hooiveld
★ 4.1k
Hi James, I am likely missing something obvious, but why is the code that I used returning a different number of genes having a GOALL-BP a…
Comment: When doing differential methylation using the sesame package, seems to only go
by
James W. MacDonald
67k
I use `minfi` for preprocessing and `DMRcate` for DMR. I like `preprocessFunnorm` (and possibly the XY-interpolated version in the `wateRme…
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
by
James W. MacDonald
67k
I gave you busted SQL code that returned the central key for the DB rather than the gene IDs. Here's the corrected version. ``` > mgis <- …
Votes
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
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