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18
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 29 days ago
shepherl
3.9k
0
votes
7
replies
742
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 23 days ago
shepherl
3.9k
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
7
votes
37
replies
5.7k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 5 hours ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 22 hours ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 25 days ago by
lauryfriese932
• 0 • written 19 months ago by
Maria Doyle
▴ 70
2
votes
4
replies
274
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 24 days ago by
James W. MacDonald
65k • written 28 days ago by
Mirella Aurora
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 28 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 11 days ago
Henrik Bengtsson
★ 2.4k
3
votes
4
replies
264
views
Store output of matchPWM()
biostrings
Biostrings
15 days ago • updated 3 days ago
mat149
▴ 70
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
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 24 days ago
shepherl
3.9k
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
6
replies
281
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 12 days ago by
swbarnes2
★ 1.4k • written 14 days ago by
arfranco
▴ 130
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 28 days ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
0
votes
4
replies
291
views
DEG with low counts
DESeq2
updated 27 days ago by
Michael Love
42k • written 4 weeks ago by
Rajat
• 0
4
votes
9
replies
487
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 9 days ago
Juan Higareda
• 0
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 16 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
2
replies
156
views
DESeq2 v1.35.0
DESeq2
updated 14 days ago by
Michael Love
42k • written 14 days ago by
Espresso
• 0
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
3
votes
3
replies
365
views
permutation test in edgeR
rna-seq
edgeR
updated 25 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
0
votes
3
replies
173
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
bas_work
▴ 30
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
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
2
replies
209
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
sansan
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 16 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
26 days ago • updated 15 days ago
Chris
▴ 10
1
vote
2
replies
103
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
2 days ago • updated 1 day ago
Daniel
• 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
5
replies
321
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 22 days ago by
James W. MacDonald
65k • written 25 days ago by
Gayatri
• 0
0
votes
7
replies
352
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
29 days ago • updated 23 days ago
hortense96
• 0
4
votes
2
replies
617
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
14 days ago • updated 10 days ago
gene_bioconductor
▴ 10
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 28 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 24 days ago by
James W. MacDonald
65k • written 27 days ago by
John
• 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
1
vote
2
replies
72
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
1 day ago
Patadù
▴ 10
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
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
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 8 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
1
vote
2
replies
173
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
22 days ago • updated 21 days ago
ATpoint
★ 4.1k
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
i.sudbery
▴ 40
0
votes
2
replies
164
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
16 days ago • updated 13 days ago
Aurora
• 0
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 24 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
283
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
16 days ago • updated 15 days ago
Yveto
• 0
0
votes
1
reply
167
views
ATACseq merge peaks
DiffBind
updated 20 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Shloka
• 0
1
vote
7
replies
355
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
21 days ago • updated 20 days ago
pl23
• 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
1
vote
1
reply
151
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 days ago by
Leo Lahti
▴ 40 • written 20 days ago by
Dario Strbenac
★ 1.5k
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 29 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
194 results • Page
1 of 4
Recent ...
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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