3
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18
replies
2.8k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 5 days ago shepherl 3.8k
0
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6
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584
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News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
7 weeks ago • updated 3 days ago shepherl 3.8k
0
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3
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1.1k
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News: European Bioconductor Conference 2023 planning
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updated 1 day ago by • 0 • written 18 months ago by ▴ 70
12
votes
12
replies
715
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Why p value inconsistent when using different number of pathway score?
limma
updated 1 day ago by ★ 3.3k • written 2 days ago by • 0
5
votes
14
replies
2.2k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
3
replies
91
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 3 days ago by 65k • written 3 days ago by ▴ 30
2
votes
2
replies
126
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 4 days ago by 65k • written 4 days ago by • 0
0
votes
4
replies
225
views
DEG with low counts
DESeq2
updated 4 days ago by 41k • written 8 days ago by • 0
0
votes
18
replies
2.4k
views
problem installing ENmix package
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written 3.1 years ago by • 0
11
votes
5
replies
7.3k
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Theoretical WGCNA Question
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updated 4 days ago by • 0 • written 9.1 years ago by ▴ 150
4
votes
8
replies
329
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Memory errors using read.bismark?
dmrseq bsseq
updated 4 days ago by ▴ 740 • written 12 days ago by • 0
0
votes
4
replies
144
views
flowStats Search Error
flowStats
updated 6 days ago by 3.8k • written 7 days ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 4 days ago by • 0 • written 8.8 years ago by ▴ 30
3
votes
3
replies
280
views
permutation test in edgeR
rna-seq edgeR
updated 2 days ago by 50k • written 15 days ago by • 0
1
vote
4
replies
108
views
Error EPICv2 ChAMP
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updated 20 hours ago by 65k • written 4 days ago by • 0
6
votes
12
replies
4.6k
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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
5 months ago • updated 23 hours ago shepherl 3.8k
0
votes
4
replies
121
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 days ago sropri • 0
0
votes
2
replies
894
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by • 0
0
votes
1
reply
103
views
Log-cpm values from limma
limma edgeR RNASeq
updated 4 days ago by 50k • written 5 days ago by • 0
0
votes
2
replies
81
views
How to make DGEList and design matrix by edgeR package
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4 days ago prity6459 • 0
0
votes
3
replies
117
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 4 days ago by 50k • written 4 days ago by • 0
6
votes
5
replies
392
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC minifi
written 7 weeks ago by • 0
0
votes
3
replies
114
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 10 minutes ago by 65k • written 1 day ago by • 0
1
vote
2
replies
104
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
6 days ago Ana • 0
0
votes
1
reply
114
views
SNP locus package for mouse?
SNPlocs packFinder
updated 6 days ago by 65k • written 9 days ago by • 0
0
votes
4
replies
562
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 6 days ago by 41k • written 6 months ago by • 0
2
votes
5
replies
1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 6 days ago by • 0 • written 10 months ago by • 0
0
votes
2
replies
880
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Single-Cell Data Simulation from Bulk RNA-seq
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updated 5 days ago by • 0 • written 17 months ago by • 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 5 days ago by 50k • written 6 months ago by ▴ 10
3
votes
3
replies
163
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Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
11 days ago • updated 5 days ago jacques.imbert • 0
0
votes
1
reply
107
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 5 days ago by ★ 4.0k • written 6 days ago by • 0
5
votes
9
replies
841
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Light difference when using coef vs omit a group when compare 3 groups.
limma
12 days ago • updated 4 days ago Chris • 0
0
votes
1
reply
102
views
covariate with negative and positive values
DESeq2
updated 4 days ago by 41k • written 6 days ago by • 0
0
votes
1
reply
86
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
0
votes
1
reply
75
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 days ago by 41k • written 5 days ago by • 0
0
votes
1
reply
79
views
rlog transformation
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
0
votes
1
reply
109
views
Adding columns to DEXSeqResults object
DEXSeq
updated 4 days ago by ★ 1.9k • written 6 days ago by • 0
0
votes
1
reply
72
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 4 days ago by ★ 1.9k • written 5 days ago by • 0
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 4 days ago by • 0 • written 14 months ago by ▴ 10
2
votes
5
replies
692
views
DESeq2 setting significant p-value
DESeq2
updated 3 days ago by 41k • written 5.0 years ago by ▴ 10
0
votes
7
replies
383
views
DESeq filtering specific to contrasts
DESeq2
updated 3 days ago by 41k • written 9 weeks ago by • 0
1
vote
2
replies
214
views
How to retrieve detailed regression results from deseq2
DESeq2
12 days ago • updated 3 days ago Weiqian ▴ 10
0
votes
2
replies
762
views
Job: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor artificialintelligence JobPosting machinelearning
written 7 months ago by 50k
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
24 days ago • updated 2 days ago Chris • 0
0
votes
2
replies
132
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
3 days ago • updated 1 day ago catv • 0
3
votes
2
replies
133
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 1 day ago by ★ 3.9k • written 3 days ago by • 0
0
votes
1
reply
69
views
FDR via q-value
qvalue
updated 23 hours ago by 65k • written 3 days ago by • 0
3
votes
6
replies
297
views
FilterByExpr low counts with small sample size
edgeR
5 days ago • updated 21 hours ago Jonathan ▴ 10
0
votes
1
reply
65
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 13 hours ago by 50k • written 14 hours ago by • 0
1
vote
2
replies
903
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 10 hours ago by ▴ 170 • written 13 months ago by ▴ 10
75 results • Page 1 of 2
Recent ...
Replies
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates by hortense96 • 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Answer: minfi::read.metharray.exp by Basti ▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none by WardDeb • 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Votes
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
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