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27
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
4 hours ago • updated 3 hours ago
shaunpeterson
• 0
0
votes
3
replies
59
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 5 hours ago by
damian.szk
▴ 80 • written 8 hours ago by
ninidea
• 0
0
votes
0
replies
25
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
10 hours ago
Ken C
• 0
0
votes
0
replies
24
views
Minor alleles giving NA from R biomart getBM?
biomaRt
minoralleledata
grch38
getBM
12 hours ago • updated 11 hours ago
Jeremy.Clark
• 0
0
votes
2
replies
87
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
1 day ago
makala
• 0
2
votes
2
replies
321
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
5 days ago • updated 1 day ago
Matthew Thornton
▴ 360
0
votes
0
replies
38
views
determine k during RUVSeq
RUVSeq
RUVnormalize
1 day ago
Ειρήνη
• 0
2
votes
3
replies
88
views
Problem installing ChAMP on a MacBook
ChAMP
updated 1 day ago by
shepherl
3.9k • written 1 day ago by
Galia
• 0
0
votes
0
replies
38
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
1 day ago
Shaimaa Gamal
• 0
0
votes
0
replies
13
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
1 day ago
oliverelijhan
0
0
votes
0
replies
54
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
1 day ago
Anton01
• 0
0
votes
0
replies
32
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
1 day ago
danalvoronov
▴ 10
0
votes
0
replies
31
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
1 day ago
k200987
• 0
2
votes
5
replies
187
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
2 days ago • updated 12 hours ago
Patadù
▴ 10
0
votes
4
replies
114
views
error running enricher from clusterprofiler
clusterProfiler
cluster
2 days ago
Yael
• 0
2
votes
3
replies
111
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
Guillermo
• 0
2
votes
1
reply
60
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 2 days ago by
Alejandro Reyes
★ 1.9k • written 4 days ago by
Sara
• 0
4
votes
9
replies
224
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 1 day ago by
ATpoint
★ 4.1k • written 2 days ago by
pangtaihin
• 0
0
votes
0
replies
28
views
Difference in Contrast in DiffBind
DiffBind
2 days ago
zzrammal
• 0
1
vote
2
replies
81
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
2 days ago
Patadù
▴ 10
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
3
replies
97
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 2 days ago by
Michael Love
42k • written 3 days ago by
Kasper
• 0
0
votes
2
replies
112
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 3 days ago by
zhouwanding
▴ 10 • written 5 days ago by
Seungmin
• 0
1
vote
0
replies
318
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
8 weeks ago • updated 3 days ago
shepherl
3.9k
1
vote
2
replies
111
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
3 days ago • updated 2 days ago
Daniel
• 0
0
votes
1
reply
80
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 3 days ago by
Michael Love
42k • written 4 days ago by
piemmea
• 0
0
votes
1
reply
58
views
Retrieving ceRNA data from the starBase or ENCORI Web API
microRNA
starBase
ceRNA
WebAPI
ENCORI
3 days ago • updated 2 days ago
Bhavya
• 0
1
vote
0
replies
49
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
3 days ago
Aleena
▴ 30
0
votes
0
replies
45
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
3 days ago
Researcher
• 0
0
votes
8
replies
473
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 2 days ago by
BioinfGuru
▴ 30 • written 4 days ago by
Eric Katagirya
• 0
1
vote
3
replies
223
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
Ashley
• 0
3
votes
4
replies
266
views
Store output of matchPWM()
biostrings
Biostrings
16 days ago • updated 3 days ago
mat149
▴ 70
1
vote
2
replies
217
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
3 days ago • updated 1 day ago
BioinfGuru
▴ 30
0
votes
2
replies
83
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
4 days ago • updated 3 days ago
Yveto
• 0
0
votes
1
reply
114
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 4 days ago by
Guido Hooiveld
★ 4.0k • written 5 days ago by
aogunbaw
• 0
0
votes
3
replies
146
views
ChAMP installation issue
Cha
ChAMP
4 days ago • updated 3 days ago
e1271094
• 0
0
votes
3
replies
8.5k
views
SingleR Label.Ont
SingleR
updated 6 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
2
votes
7
replies
357
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
9 days ago • updated 6 days ago
sajadahmad41454
• 0
2
votes
2
replies
267
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
10 days ago • updated 4 days ago
zzrammal
• 0
4
votes
5
replies
313
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
11 days ago • updated 2 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 3 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
4
replies
364
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by
Ziliang
• 0 • written 16 days ago by
Ian D.
▴ 70
1
vote
2
replies
202
views
Citation for edgeR user guide
edgeR
written 24 days ago by
k___
▴ 30
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 12 hours ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
0
votes
2
replies
747
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 1 day ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
7
votes
38
replies
5.7k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 14 hours ago by
Johannes Rainer
★ 2.0k • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
0
votes
2
replies
945
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 2 days ago by
mariakenneth147
• 0 • written 17 months ago by
pharamac
• 0
2
votes
3
replies
1.7k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 4 days ago by
bandconductor
• 0 • written 3.6 years ago by
ZheFrench
▴ 60
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 2 days ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 5 hours ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters
by
anne-laure
• 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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