0
votes
7
replies
743
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
11 weeks ago • updated 24 days ago shepherl 3.9k
7
votes
38
replies
5.7k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 12 hours ago by ★ 2.0k • written 5.5 years ago by ★ 4.0k
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 1 day ago by ▴ 220 • written 6.7 years ago by ▴ 80
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 3 days ago by 42k • written 15 months ago by • 0
1
vote
2
replies
396
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 13 days ago by 50k • written 13 days ago by • 0
2
votes
4
replies
279
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 25 days ago by 65k • written 29 days ago by • 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 29 days ago by • 0 • written 8.9 years ago by ▴ 30
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 17 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.2 years ago by • 0
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro clustering
updated 4 hours ago by • 0 • written 7.9 years ago by • 0
3
votes
3
replies
367
views
permutation test in edgeR
rna-seq edgeR
updated 26 days ago by 50k • written 5 weeks ago by • 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 28 days ago by • 0 • written 9.2 years ago by ▴ 150
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 ★ 6.5k • written 11 days ago by • 0
4
votes
5
replies
313
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
11 days ago • updated 2 days ago Chris ▴ 10
3
votes
4
replies
266
views
Store output of matchPWM()
biostrings Biostrings
16 days ago • updated 3 days ago mat149 ▴ 70
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 17 days ago by • 0 • written 13.1 years ago by ▴ 10
0
votes
6
replies
285
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 13 days ago by ★ 1.4k • written 14 days ago by ▴ 130
0
votes
4
replies
1.2k
views
News: European Bioconductor Conference 2023 planning
Europe Conference EuroBioC Events News
updated 10 hours ago by • 0 • written 19 months ago by ▴ 70
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 25 days ago shepherl 3.9k
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
27 days ago • updated 16 days ago Chris ▴ 10
0
votes
2
replies
112
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 3 days ago by ▴ 10 • written 5 days ago by • 0
0
votes
3
replies
8.5k
views
SingleR Label.Ont
SingleR
updated 6 days ago by • 0 • written 8 months ago by • 0
0
votes
4
replies
291
views
DEG with low counts
DESeq2
updated 28 days ago by 42k • written 4 weeks ago by • 0
4
votes
9
replies
489
views
Memory errors using read.bismark?
dmrseq bsseq
5 weeks ago • updated 10 days ago Juan Higareda • 0
0
votes
2
replies
159
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 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
0
votes
3
replies
173
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 28 days ago by 65k • written 28 days ago by ▴ 30
2
votes
2
replies
210
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 28 days ago by 65k • written 28 days ago by • 0
2
votes
2
replies
301
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 1 day ago Matthew Thornton ▴ 360
0
votes
1
reply
134
views
putting my own expression data in deseq2
DESeq2
updated 17 days ago by ★ 4.1k • written 17 days ago by • 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 7 days ago by • 0 • written 15 months ago by ▴ 10
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 days ago by 42k • written 11 days ago by ▴ 70
2
votes
1
reply
60
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 2 days ago by ★ 1.9k • written 4 days ago by • 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 9 days ago by • 0 • written 5 months ago by • 0
0
votes
2
replies
165
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
17 days ago • updated 14 days ago Aurora • 0
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
14 days ago • updated 11 days ago gene_bioconductor ▴ 10
0
votes
7
replies
360
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 24 days ago hortense96 • 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 ▴ 180 • written 14 months ago by ▴ 10
1
vote
2
replies
111
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
3 days ago • updated 2 days ago Daniel • 0
3
votes
3
replies
244
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
5 weeks ago • updated 29 days ago jacques.imbert • 0
1
vote
3
replies
221
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 50k • written 3 days ago by • 0
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 25 days ago by 65k • written 28 days ago by • 0
1
vote
2
replies
211
views
Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 11 days ago Lluís Revilla Sancho ▴ 730
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by 42k • written 23 days ago by ▴ 20
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 9 days ago by 50k • written 5.6 years ago by ▴ 10
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 21 days ago by 65k • written 22 days ago by • 0
5
votes
9
replies
973
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 29 days ago Chris ▴ 10
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 22 days ago by 42k • written 23 days ago by • 0
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 42k • written 24 days ago by ▴ 40
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
192 results • Page 1 of 4
Recent ...
Replies
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$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
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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