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Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
3 hours ago • updated 2 hours ago
Patadù
▴ 10
0
votes
3
replies
61
views
error running enricher from clusterprofiler
clusterProfiler
cluster
updated 4 hours ago by
Guido Hooiveld
★ 4.0k • written 7 hours ago by
Yael
• 0
2
votes
3
replies
63
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 4 hours ago by
ATpoint
★ 4.1k • written 6 hours ago by
Guillermo
• 0
2
votes
1
reply
45
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 6 hours ago by
Alejandro Reyes
★ 1.9k • written 2 days ago by
Sara
• 0
0
votes
2
replies
51
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 7 hours ago by
ATpoint
★ 4.1k • written 10 hours ago by
pangtaihin
• 0
0
votes
0
replies
18
views
Difference in Contrast in DiffBind
DiffBind
9 hours ago
zzrammal
• 0
1
vote
2
replies
65
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
11 hours ago • updated 7 hours ago
Patadù
▴ 10
10
votes
9
replies
1.8k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 10 hours ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
3
replies
74
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 7 hours ago by
Michael Love
42k • written 23 hours ago by
Kasper
• 0
0
votes
2
replies
93
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 1 day ago by
zhouwanding
▴ 10 • written 3 days ago by
Seungmin
• 0
1
vote
0
replies
305
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
7 weeks ago • updated 1 day ago
shepherl
3.9k
1
vote
2
replies
73
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
1 day ago • updated 2 hours ago
Daniel
• 0
0
votes
1
reply
58
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 1 day ago by
Michael Love
42k • written 2 days ago by
piemmea
• 0
0
votes
1
reply
45
views
Retrieving ceRNA data from the starBase or ENCORI Web API
microRNA
starBase
ceRNA
WebAPI
ENCORI
1 day ago • updated 10 minutes ago
Bhavya
• 0
1
vote
0
replies
33
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
1 day ago
Aleena
▴ 30
0
votes
0
replies
31
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
1 day ago
Researcher
• 0
0
votes
8
replies
428
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 21 hours ago by
BioinfGuru
▴ 30 • written 2 days ago by
Eric Katagirya
• 0
1
vote
3
replies
202
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 19 hours ago by
Gordon Smyth
50k • written 1 day ago by
Ashley
• 0
3
votes
4
replies
246
views
Store output of matchPWM()
biostrings
Biostrings
14 days ago • updated 1 day ago
mat149
▴ 70
0
votes
1
reply
46
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
updated 1 day ago by
Michael Love
42k • written 1 day ago by
BioinfGuru
▴ 30
0
votes
2
replies
66
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
2 days ago • updated 1 day ago
Yveto
• 0
0
votes
1
reply
79
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 2 days ago by
Guido Hooiveld
★ 4.0k • written 3 days ago by
aogunbaw
• 0
0
votes
3
replies
124
views
ChAMP installation issue
Cha
ChAMP
2 days ago • updated 1 day ago
e1271094
• 0
0
votes
1
reply
213
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
3 days ago • updated 1 day ago
Matthew Thornton
▴ 350
0
votes
3
replies
8.2k
views
SingleR Label.Ont
SingleR
updated 4 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
1
reply
125
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 5 days ago by
ATpoint
★ 4.1k • written 5 days ago by
sajadahmad41454
• 0
1
vote
2
replies
227
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
6 days ago • updated 5 days ago
Dylan.Sheerin
• 0
0
votes
0
replies
53
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
5 days ago
neilzhao
▴ 30
0
votes
1
reply
87
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
sajadahmad41454
• 0
3
votes
4
replies
491
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 7 days ago by
Mike Smith
★ 6.5k • written 9 days ago by
robersy
• 0
2
votes
7
replies
336
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
7 days ago • updated 4 days ago
sajadahmad41454
• 0
0
votes
0
replies
58
views
Treeio as.treedata function seq lenght error
treeio
7 days ago
nromerov
• 0
2
votes
2
replies
250
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
8 days ago • updated 2 days ago
zzrammal
• 0
3
votes
10
replies
421
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 5 days ago by
James W. MacDonald
65k • written 8 days ago by
Abbey
• 0
2
votes
1
reply
144
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
e1271094
• 0
0
votes
1
reply
94
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 8 days ago by
shepherl
3.9k • written 8 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
74
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
8 days ago
Dinesh
• 0
3
votes
5
replies
270
views
Help with running egsea()
EGSEA
9 days ago • updated 7 days ago
Chris
▴ 10
3
votes
1
reply
135
views
How to save the DEXSeq results
DEXSeq
updated 9 days ago by
Michael Love
42k • written 9 days ago by
Sara
• 0
4
votes
5
replies
293
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
9 days ago • updated 5 hours ago
Chris
▴ 10
0
votes
3
replies
203
views
Couldn't connect to server while using "pathways"
graphite
updated 8 days ago by
Michael Love
42k • written 9 days ago by
fduguchunhui
• 0
1
vote
1
reply
125
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 9 days ago by
Michael Love
42k • written 9 days ago by
mat149
▴ 70
1
vote
1
reply
176
views
Handling multiple differential expression comparisons
DESeq2
updated 10 days ago by
Michael Love
42k • written 12 days ago by
Zainab
▴ 10
2
votes
2
replies
214
views
fgsea significant result
fgsea
10 days ago
Chris
▴ 10
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 1 day ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
6
replies
276
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 11 days ago by
swbarnes2
★ 1.4k • written 12 days ago by
arfranco
▴ 130
1
vote
2
replies
388
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 11 days ago by
Gordon Smyth
50k • written 11 days ago by
Kim
• 0
2
votes
3
replies
252
views
package goseq seems to be not available on the latest version of R
goseq
updated 9 days ago by
Gordon Smyth
50k • written 11 days ago by
Patrycja
▴ 20
2
votes
3
replies
243
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 10 days ago by
ATpoint
★ 4.1k • written 12 days ago by
Reza
• 0
0
votes
0
replies
111
views
dba.plotProfile() plotting and interpretation
DiffBind
12 days ago
Henry
▴ 10
1,000 results • Page
1 of 20
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Replies
Comment: Create protein sequences including variants from a VCF file
by
Yun
• 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization?
by
Daniel
• 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Guido Hooiveld
★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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