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0
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2
replies
65
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DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
11 hours ago • updated 8 hours ago
makala
• 0
0
votes
0
replies
27
views
determine k during RUVSeq
RUVSeq
RUVnormalize
14 hours ago
Ειρήνη
• 0
0
votes
0
replies
21
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
15 hours ago
Shaimaa Gamal
• 0
0
votes
0
replies
12
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
16 hours ago
oliverelijhan
0
0
votes
0
replies
35
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
18 hours ago
Anton01
• 0
2
votes
3
replies
72
views
Problem installing ChAMP on a MacBook
ChAMP
updated 15 hours ago by
shepherl
3.9k • written 23 hours ago by
Galia
• 0
0
votes
0
replies
23
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
26
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
1 day ago
k200987
• 0
1
vote
4
replies
151
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
updated 1 day ago by
Marcel Ramos
690 • written 1 day ago by
Patadù
▴ 10
0
votes
4
replies
105
views
error running enricher from clusterprofiler
clusterProfiler
cluster
1 day ago
Yael
• 0
2
votes
3
replies
100
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
Guillermo
• 0
0
votes
0
replies
25
views
Difference in Contrast in DiffBind
DiffBind
1 day ago
zzrammal
• 0
4
votes
9
replies
210
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 14 hours ago by
ATpoint
★ 4.1k • written 1 day ago by
pangtaihin
• 0
1
vote
2
replies
72
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
1 day ago
Patadù
▴ 10
0
votes
3
replies
86
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 1 day ago by
Michael Love
42k • written 2 days ago by
Kasper
• 0
1
vote
2
replies
103
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
2 days ago • updated 1 day ago
Daniel
• 0
0
votes
1
reply
52
views
Retrieving ceRNA data from the starBase or ENCORI Web API
microRNA
starBase
ceRNA
WebAPI
ENCORI
2 days ago • updated 1 day ago
Bhavya
• 0
1
vote
0
replies
43
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
2 days ago
Aleena
▴ 30
0
votes
0
replies
40
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
2 days ago
Researcher
• 0
1
vote
3
replies
215
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
1
vote
2
replies
150
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
3 days ago • updated 8 hours ago
BioinfGuru
▴ 30
0
votes
8
replies
457
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 3 days ago by
Eric Katagirya
• 0
0
votes
1
reply
73
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 2 days ago by
Michael Love
42k • written 3 days ago by
piemmea
• 0
0
votes
2
replies
77
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
3 days ago • updated 2 days ago
Yveto
• 0
2
votes
1
reply
54
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 3 days ago by
Sara
• 0
0
votes
3
replies
136
views
ChAMP installation issue
Cha
ChAMP
3 days ago • updated 2 days ago
e1271094
• 0
0
votes
1
reply
101
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 3 days ago by
Guido Hooiveld
★ 4.0k • written 4 days ago by
aogunbaw
• 0
0
votes
2
replies
104
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 2 days ago by
zhouwanding
▴ 10 • written 4 days ago by
Seungmin
• 0
2
votes
2
replies
258
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 10 hours ago
Matthew Thornton
▴ 360
0
votes
1
reply
151
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
sajadahmad41454
• 0
0
votes
0
replies
63
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
7 days ago
neilzhao
▴ 30
0
votes
1
reply
95
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
sajadahmad41454
• 0
1
vote
2
replies
247
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
8 days ago • updated 7 days ago
Dylan.Sheerin
• 0
2
votes
7
replies
352
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
8 days ago • updated 5 days ago
sajadahmad41454
• 0
0
votes
0
replies
65
views
Treeio as.treedata function seq lenght error
treeio
9 days ago
nromerov
• 0
2
votes
2
replies
262
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
9 days ago • updated 3 days ago
zzrammal
• 0
3
votes
10
replies
433
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 6 days ago by
James W. MacDonald
65k • written 9 days ago by
Abbey
• 0
0
votes
1
reply
99
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 9 days ago by
shepherl
3.9k • written 9 days ago by
cyril.dalmasso
• 0
2
votes
1
reply
155
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
e1271094
• 0
0
votes
0
replies
82
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
10 days ago
Dinesh
• 0
3
votes
5
replies
282
views
Help with running egsea()
EGSEA
10 days ago • updated 9 days ago
Chris
▴ 10
3
votes
1
reply
142
views
How to save the DEXSeq results
DEXSeq
updated 10 days ago by
Michael Love
42k • written 10 days ago by
Sara
• 0
2
votes
1
reply
139
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 10 days ago by
Michael Love
42k • written 10 days ago by
mat149
▴ 70
0
votes
3
replies
215
views
Couldn't connect to server while using "pathways"
graphite
updated 10 days ago by
Michael Love
42k • written 10 days ago by
fduguchunhui
• 0
4
votes
5
replies
310
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
11 days ago • updated 1 day ago
Chris
▴ 10
3
votes
4
replies
501
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 8 days ago by
Mike Smith
★ 6.5k • written 11 days ago by
robersy
• 0
2
votes
2
replies
221
views
fgsea significant result
fgsea
12 days ago • updated 11 days ago
Chris
▴ 10
1
vote
2
replies
395
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
Kim
• 0
2
votes
3
replies
261
views
package goseq seems to be not available on the latest version of R
goseq
updated 10 days ago by
Gordon Smyth
50k • written 13 days ago by
Patrycja
▴ 20
2
votes
3
replies
251
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 11 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Reza
• 0
45,663 results • Page
1 of 914
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Replies
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
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
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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