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2
replies
74
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DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
15 hours ago • updated 12 hours ago
makala
• 0
2
votes
2
replies
263
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 14 hours ago
Matthew Thornton
▴ 360
0
votes
0
replies
30
views
determine k during RUVSeq
RUVSeq
RUVnormalize
18 hours ago
Ειρήνη
• 0
2
votes
3
replies
76
views
Problem installing ChAMP on a MacBook
ChAMP
updated 19 hours ago by
shepherl
3.9k • written 1 day ago by
Galia
• 0
0
votes
0
replies
25
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
19 hours ago
Shaimaa Gamal
• 0
0
votes
0
replies
12
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
20 hours ago
oliverelijhan
0
0
votes
0
replies
41
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
22 hours ago
Anton01
• 0
0
votes
0
replies
26
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
154
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
106
views
error running enricher from clusterprofiler
clusterProfiler
cluster
1 day ago
Yael
• 0
2
votes
3
replies
102
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
2
votes
1
reply
56
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
4
votes
9
replies
212
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 19 hours ago by
ATpoint
★ 4.1k • written 1 day ago by
pangtaihin
• 0
0
votes
0
replies
25
views
Difference in Contrast in DiffBind
DiffBind
1 day ago
zzrammal
• 0
1
vote
2
replies
73
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
2 days ago • updated 1 day 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
88
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
0
votes
2
replies
108
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 2 days ago by
zhouwanding
▴ 10 • written 4 days ago by
Seungmin
• 0
1
vote
0
replies
314
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
7 weeks ago • updated 2 days ago
shepherl
3.9k
1
vote
2
replies
106
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
2 days ago • updated 1 day ago
Daniel
• 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
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
44
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
2 days ago
Aleena
▴ 30
0
votes
0
replies
41
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
3 days ago
Researcher
• 0
0
votes
8
replies
464
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
1
vote
3
replies
216
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
264
views
Store output of matchPWM()
biostrings
Biostrings
15 days ago • updated 3 days ago
mat149
▴ 70
1
vote
2
replies
172
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
3 days ago • updated 12 hours ago
BioinfGuru
▴ 30
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
0
votes
1
reply
103
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
3
replies
139
views
ChAMP installation issue
Cha
ChAMP
4 days ago • updated 2 days ago
e1271094
• 0
0
votes
3
replies
8.4k
views
SingleR Label.Ont
SingleR
updated 5 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
1
reply
153
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
sajadahmad41454
• 0
2
votes
7
replies
354
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
8 days ago • updated 5 days ago
sajadahmad41454
• 0
2
votes
2
replies
263
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
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
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 2 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
4
replies
358
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by
Ziliang
• 0 • written 15 days ago by
Ian D.
▴ 70
1
vote
2
replies
201
views
Citation for edgeR user guide
edgeR
written 23 days ago by
k___
▴ 30
0
votes
2
replies
746
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 1 hour ago by
Johannes Rainer
★ 2.0k • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
1
vote
5
replies
513
views
Can't post a question containing code?
Bioconductor
updated 6 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
0
votes
2
replies
942
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 1 day ago by
mariakenneth147
• 0 • written 17 months ago by
pharamac
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 6 days ago by
maria.soler
• 0 • written 15 months ago by
kalavattam
▴ 10
2
votes
3
replies
1.7k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 3 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 1 day ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
48 results • Page
1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
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…
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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