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47
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
14 hours ago • updated 13 hours ago
shaunpeterson
• 0
0
votes
3
replies
77
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 15 hours ago by
damian.szk
▴ 80 • written 18 hours ago by
ninidea
• 0
0
votes
2
replies
110
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 2 hours ago by
JKim
• 0 • written 21 hours ago by
Ken C
• 0
0
votes
0
replies
29
views
Minor alleles giving NA from R biomart getBM?
biomaRt
minoralleledata
grch38
getBM
22 hours ago
Jeremy.Clark
• 0
0
votes
2
replies
97
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
1 day ago
makala
• 0
2
votes
2
replies
348
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
6 days ago • updated 1 day ago
Matthew Thornton
▴ 360
0
votes
0
replies
43
views
determine k during RUVSeq
RUVSeq
RUVnormalize
1 day ago
Ειρήνη
• 0
2
votes
3
replies
92
views
Problem installing ChAMP on a MacBook
ChAMP
updated 1 day ago by
shepherl
3.9k • written 2 days ago by
Galia
• 0
0
votes
0
replies
43
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
1 day ago
Shaimaa Gamal
• 0
0
votes
0
replies
14
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
1 day ago
oliverelijhan
0
0
votes
0
replies
57
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
1 day ago
Anton01
• 0
0
votes
0
replies
36
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
2 days ago
danalvoronov
▴ 10
0
votes
0
replies
33
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
2 days ago
k200987
• 0
2
votes
5
replies
204
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
2 days ago • updated 22 hours ago
Patadù
▴ 10
0
votes
4
replies
120
views
error running enricher from clusterprofiler
clusterProfiler
cluster
2 days ago
Yael
• 0
2
votes
3
replies
114
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
Guillermo
• 0
2
votes
1
reply
66
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
230
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
30
views
Difference in Contrast in DiffBind
DiffBind
2 days ago
zzrammal
• 0
1
vote
2
replies
84
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
3 days ago • updated 2 days ago
Patadù
▴ 10
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 2 days ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
3
replies
102
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
121
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
320
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
118
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
3 days ago • updated 2 days ago
Daniel
• 0
0
votes
1
reply
83
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
64
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
53
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
3 days ago
Aleena
▴ 30
0
votes
0
replies
47
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
4 days ago
Researcher
• 0
0
votes
8
replies
483
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 3 days ago by
BioinfGuru
▴ 30 • written 4 days ago by
Eric Katagirya
• 0
1
vote
3
replies
232
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
Ashley
• 0
3
votes
4
replies
270
views
Store output of matchPWM()
biostrings
Biostrings
16 days ago • updated 4 days ago
mat149
▴ 70
1
vote
2
replies
225
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
4 days ago • updated 1 day ago
BioinfGuru
▴ 30
0
votes
2
replies
90
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
122
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
154
views
ChAMP installation issue
Cha
ChAMP
5 days ago • updated 3 days ago
e1271094
• 0
0
votes
3
replies
8.6k
views
SingleR Label.Ont
SingleR
updated 6 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
1
reply
160
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
sajadahmad41454
• 0
1
vote
2
replies
255
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
9 days ago • updated 8 days ago
Dylan.Sheerin
• 0
0
votes
0
replies
68
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
8 days ago
neilzhao
▴ 30
0
votes
1
reply
99
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
3
votes
4
replies
505
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 9 days ago by
Mike Smith
★ 6.5k • written 12 days ago by
robersy
• 0
2
votes
7
replies
363
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
9 days ago • updated 6 days ago
sajadahmad41454
• 0
0
votes
0
replies
69
views
Treeio as.treedata function seq lenght error
treeio
10 days ago
nromerov
• 0
2
votes
2
replies
269
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
3
votes
10
replies
441
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 7 days ago by
James W. MacDonald
65k • written 10 days ago by
Abbey
• 0
2
votes
1
reply
163
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 10 days ago by
James W. MacDonald
65k • written 11 days ago by
e1271094
• 0
0
votes
1
reply
103
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 10 days ago by
shepherl
3.9k • written 10 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
87
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 days ago
Dinesh
• 0
3
votes
5
replies
289
views
Help with running egsea()
EGSEA
11 days ago • updated 10 days ago
Chris
▴ 10
1,000 results • Page
1 of 20
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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" …
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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