3
votes
4
replies
3.8k
views
R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
error mac DESeq2 GenomeInfoDb R
5.0 years ago • updated 4.9 years ago Dan ▴ 20
6
votes
5
replies
1.7k
views
perform DESeq2 based on paired sample
DESeq2
4.9 years ago xiaofeiwang18266 ▴ 60
3
votes
2
replies
3.5k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.9 years ago camerond • 0
4
votes
4
replies
1.6k
views
DEseq2: working with unbalanced number of sample in tumor study?
Deseq2 RNASeqRData unbalancedsamplesize
updated 3.6 years ago by 43k • written 4.9 years ago by • 0
3
votes
9
replies
2.3k
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
4.9 years ago Daniel.Schnell • 0
2
votes
2
replies
1.6k
views
DESeq2 in R
DESeq2 apeglm
updated 4.9 years ago by ★ 1.4k • written 4.9 years ago by ▴ 10
2
votes
3
replies
2.5k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 30
0
votes
1
reply
1.5k
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl Alignment QuasR
updated 4.9 years ago by ▴ 350 • written 4.9 years ago by • 0
4
votes
9
replies
2.1k
views
Variance stabilising transformation to within given range
DESeq2 scaling vst
updated 4.8 years ago by ★ 13k • written 4.9 years ago by ▴ 60
1
vote
2
replies
660
views
DESeq2
DESeq2
4.9 years ago amoaristotle ▴ 10
1
vote
4
replies
1.4k
views
DESeq2 Design formula matrix not full rank
DESeq2 matrixnotfullrank Designformula DEseq2
4.9 years ago Nicolò • 0
0
votes
2
replies
3.1k
views
Error in .testForValidKeys(x, keys, keytype, fks)
DUDAS org.At.tair.db
4.9 years ago lore • 0
0
votes
2
replies
1.7k
views
DSEQ apeglm
DESeq2 apeglm
4.9 years ago amoaristotle ▴ 10
0
votes
5
replies
2.7k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
1
vote
1
reply
2.3k
views
Error when using read.FCS
compensation flowCore FlowCore read.FCS
updated 4.9 years ago by ▴ 360 • written 4.9 years ago by • 0
1
vote
3
replies
2.1k
views
topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 4.9 years ago by ▴ 760 • written 4.9 years ago by • 0
0
votes
4
replies
2.4k
views
DEseq2: setting up the correct contrast.
DESeq2 RNASeq
updated 4.9 years ago by ★ 1.4k • written 4.9 years ago by • 0
2
votes
1
reply
1.8k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 4.9 years ago by 43k • written 4.9 years ago by ★ 5.0k
0
votes
6
replies
1.9k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
4.9 years ago rproendo ▴ 30
3
votes
11
replies
7.8k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 22 months ago by ★ 4.1k • written 4.9 years ago by • 0
0
votes
0
replies
804
views
gwascat Liftover Fails Silently
gwascat
4.9 years ago anailis • 0
0
votes
2
replies
1.3k
views
getUniqueCleavageEvents() not working in GUIDEseq package
GUIDEseq
updated 4.9 years ago by ★ 4.3k • written 4.9 years ago by • 0
3
votes
5
replies
2.0k
views
Swish (fishpond) scaled counts result
Swish fishpond
4.9 years ago • updated 4.8 years ago 675743 ▴ 20
0
votes
1
reply
1.3k
views
DSEQ for DEG in R
microbiomeExplorer tartare projectR
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 10
0
votes
7
replies
2.5k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 4.9 years ago by ▴ 980 • written 4.9 years ago by • 0
2
votes
1
reply
5.2k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 4.9 years ago by 68k • written 4.9 years ago by ★ 1.6k
1
vote
5
replies
2.9k
views
How can I use bioconductor and Deseq2 in linux ubuntu 18
RiboProfiling DESeq2 Bioconductor RNASeqRData
updated 3.2 years ago by ★ 4.0k • written 4.9 years ago by • 0
3
votes
3
replies
2.7k
views
Normalisation in DESeq2
DESeq2
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by ▴ 50
1
vote
1
reply
1.4k
views
No result from plotPCA()
DESeq2 RNASeq plotpca
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
2
votes
4
replies
2.5k
views
DESeq2 results change dramatically after scaling + centering of numeric variable
DESeq2
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 20
1
vote
2
replies
5.6k
views
Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 4.9 years ago by • 0 • written 6.0 years ago by • 0
2
votes
6
replies
1.6k
views
DESeq2 anormally high estimation of Log2FoldChange
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
votes
2
replies
1.4k
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
4.9 years ago sissialva21 • 0
0
votes
2
replies
1.4k
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
1
vote
14
replies
3.3k
views
error: DBA object is already formed from a consensus peakset
DiffBind
4.9 years ago ahua217 ▴ 10
0
votes
2
replies
1.6k
views
Error log when I use biomaRt getBM
biomaRt annotationTools
updated 4.9 years ago by ★ 6.6k • written 4.9 years ago by • 0
2
votes
3
replies
1.6k
views
Independent filtering of NGS data
independentfiltering DESeq2 CRISPR
4.9 years ago Rubén • 0
0
votes
1
reply
945
views
What does the error 'invalid class “DMNGroup” object' mean, how to resolve the problem?
DirichletMultinomial
4.9 years ago mschmidt ▴ 10
2
votes
2
replies
4.2k
views
DiffBind installation fails: Error: package ‘BiocGenerics’ 0.34.0 is loaded, but >= 0.36.0 is required by ‘IRanges’
systemPipeR Bioconductor DiffBind BiocGenerics
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
1
vote
1
reply
819
views
dba.count() of DiffBind 3.0 does not have bSubControl parameter
DiffBind
updated 4.9 years ago by ★ 5.2k • written 4.9 years ago by • 0
0
votes
1
reply
3.0k
views
BiocManager::install("EnsDb.Hsapiens.v75") install fails with non-zero exit status
biocmanager Install
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 10
0
votes
2
replies
4.3k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
4.9 years ago Emilia ▴ 40
2
votes
3
replies
2.8k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 30
3
votes
3
replies
1.7k
views
DESeq2 for time-course with nested individuals
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Question: export edgeR normalised OTU table
microbiome edgeR
4.9 years ago Pozdrawiam • 0
2
votes
0
replies
1.5k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.9 years ago Ben ▴ 50
2
votes
2
replies
2.1k
views
Calculation of logCPM in edgeR
logCPM edgeR
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 20
3
votes
4
replies
4.2k
views
Calculation of logFC in edgeR
edgeR logfc
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 20
1
vote
2
replies
1.1k
views
How to make BiocParallel work in DiffBind when working under windows system
DiffBind
updated 4.9 years ago by 25k • written 4.9 years ago by ▴ 40
0
votes
7
replies
2.5k
views
Problem with Tximport
tximportData tximport
4.9 years ago agoesmartini • 0
46,699 results • Page 137 of 934
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Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
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You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
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In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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