2
votes
28
replies
7.2k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 2.1 years ago by 68k • written 3.0 years ago by ▴ 10
0
votes
1
reply
799
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 10
2
votes
2
replies
1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.1 years ago Manthos • 0
1
vote
4
replies
1.5k
views
Can DESeq2 be used to compare groups of genes?
DESeq2
2.1 years ago pl23 • 0
0
votes
4
replies
1.0k
views
ATACseqTFEA - preparebindingSites() for whole genome?
ATACseqTFEA
updated 22 months ago by ★ 1.3k • written 2.1 years ago by • 0
0
votes
1
reply
754
views
plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
2
replies
1.0k
views
Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware SingleCellData annotationTools
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
votes
4
replies
1.6k
views
rhdf5: error trying to access files from S3 Cloud from NASA earthaccess
rhdf5
2.1 years ago Caio • 0
1
vote
7
replies
10k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 21 months ago by 16k • written 2.1 years ago by ▴ 10
2
votes
1
reply
1.4k
views
ChAMP can't be found in Bioc3.18?
ChAMP
2.1 years ago ramonfallon ▴ 20
0
votes
6
replies
3.6k
views
Error when Installing BioConductor Package ('affy')
Bioconductor Install affy
updated 2.1 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
votes
0
replies
825
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
2.1 years ago vasily.dobrovolsky • 0
0
votes
1
reply
788
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
2
votes
2
replies
1.2k
views
Predicting missing values splines DESeq2
deseq DESeq2
2.1 years ago georgii.vdovin • 0
0
votes
0
replies
613
views
GaussNorm fails to recognize flowFrames in flowSet as individual elements
flowStats
2.1 years ago mikkel.byrdal • 0
1
vote
3
replies
2.6k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 2.1 years ago by ▴ 750 • written 4.6 years ago by • 0
2
votes
0
replies
752
views
News: Bioconductor's Transition Away from Twitter/X
Bioconductor
2.1 years ago Maria Doyle ▴ 110
0
votes
1
reply
1.7k
views
sampling random regions of same nucleotide composition from hg38 genome
annotatr regioneR gkmSVM
updated 2.1 years ago by • 0 • written 5.0 years ago by ▴ 20
0
votes
10
replies
1.9k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
2.1 years ago • updated 21 months ago ScafioRuo • 0
0
votes
0
replies
1.0k
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
2.1 years ago jared.andrews07 ▴ 30
0
votes
1
reply
663
views
gene aligning reference
geneRecommender gene
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
0
replies
628
views
accesing gene name RNAseq
genetics GeneticsPed Genetics
2.1 years ago Gülsüm • 0
3
votes
5
replies
2.3k
views
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
sesame IlluminaHumanMethylationEPICv2anno.20a1.hg38 methylationEPICv2.0 EpicV2
updated 21 months ago by • 0 • written 2.1 years ago by ▴ 10
2
votes
4
replies
1.4k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.1 years ago Tyler Sagendorf ▴ 10
0
votes
1
reply
595
views
DESeq2 design with unbalance data and a multifactor design
DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
votes
0
replies
724
views
Identifying populations within a FlowSOM tree
FlowSOM
2.1 years ago agus_rizzo • 0
1
vote
2
replies
3.2k
views
trying to add SingleR label to Seurat Object fails
SingleR Seurat
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by ★ 1.5k
0
votes
4
replies
922
views
Sign Output Values PADOG
PADOG
written 2.1 years ago by • 0
0
votes
1
reply
692
views
EGSEA with Affymetrix data
EGSEA
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
3
votes
6
replies
1.6k
views
Methylation data analysis
MethylationArrayData methylationArrayAnalysis
2.1 years ago aldea85 • 0
0
votes
2
replies
1.6k
views
annotatePeak error for some problem
ChIPseeker
written 2.1 years ago by • 0
0
votes
1
reply
675
views
COTAN mantainance
BuildReport
updated 2.1 years ago by 4.2k • written 2.1 years ago by • 0
0
votes
0
replies
1.6k
views
Version map cannot be validated - not mapping to new bioconductor website
Install
2.1 years ago Alexander • 0
0
votes
0
replies
721
views
News: CRAN downtime
BiocManager Bioconductor
2.1 years ago shepherl 4.2k
0
votes
0
replies
498
views
R/sql code to find the haplotype data from patient's rsIDs
starallele phenoTest
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
2
replies
1.4k
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
2.1 years ago anton.kratz ▴ 60
0
votes
4
replies
2.1k
views
decontX (celda package)
decontX celda
updated 2.1 years ago by ▴ 30 • written 2.1 years ago by • 0
0
votes
1
reply
648
views
Incorrect display of Y-axis
trackViewer
updated 2.1 years ago by ★ 1.3k • written 2.1 years ago by • 0
0
votes
0
replies
1.2k
views
News: EMBO|EMBL Conference "AI and Biology"
EMBL Heidelberg AI Conference
2.1 years ago Wolfgang Huber ★ 13k
0
votes
1
reply
1.1k
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
votes
4
replies
2.1k
views
sesameDataCache is not work properly on my system
sesameData sesameDataCache sesame ExperimentalHub
updated 9 months ago by • 0 • written 2.1 years ago by • 0
0
votes
2
replies
916
views
combat output NaN
sva
2.1 years ago maxixian1990 • 0
2
votes
7
replies
1.7k
views
Errors with running learn.bn function and setting toCompact to TRUE in one.step.pigengene function in Pigengene package
Pigengene
2.1 years ago kjngo ▴ 40
5
votes
6
replies
2.7k
views
Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
Pigengene
2.1 years ago kjngo ▴ 40
0
votes
1
reply
900
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 2.1 years ago by ★ 13k • written 2.1 years ago by • 0
1
vote
3
replies
1.4k
views
FlowSOM Error in flowCore::read.FCS
FlowSOM
updated 2.1 years ago by ▴ 360 • written 2.1 years ago by • 0
1
vote
3
replies
1.1k
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
1
reply
838
views
gDNAx diagnostic output interpretation
gDNAx
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by • 0
0
votes
1
reply
1.3k
views
tximeta errors: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function '…
tximeta
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
votes
2
replies
874
views
Swimming downstream: transcript fold changes
DEXSeq stageR
2.1 years ago jbono ▴ 10
46,695 results • Page 38 of 934
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
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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