0
votes
0
replies
276
views
ChemmineOB avaiable for macOS Binary (arm64)?
ChemmineOB
13 months ago Simone • 0
0
votes
2
replies
763
views
installation error for BiocNeighbors package
BiocNeighbors
13 months ago 育 • 0
0
votes
0
replies
572
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP ChAMPdata
13 months ago elgomez • 0
1
vote
3
replies
883
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
0
votes
5
replies
1.2k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
0
votes
0
replies
341
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
13 months ago user_bioinfo • 0
0
votes
0
replies
603
views
Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
13 months ago kim • 0
0
votes
0
replies
404
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
13 months ago brayas13 • 0
0
votes
0
replies
329
views
export processed data from flowploidy
flowPloidy
13 months ago Zdenek Skala • 0
0
votes
0
replies
310
views
Filtering Steps for proActiv Analysis
Transcriptomics proActiv
13 months ago LuciaNhu • 0
0
votes
0
replies
398
views
diffbind covariates
DiffBind ATACSeq
updated 13 months ago by 43k • written 13 months ago by ▴ 220
0
votes
0
replies
324
views
MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
MOFA2
13 months ago mario_de_manner • 0
0
votes
0
replies
376
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
13 months ago Ibrahim • 0
0
votes
0
replies
354
views
DiffBind subset replicates
DiffBind
14 months ago Haiping • 0
0
votes
0
replies
446
views
Rsubread - sublong function
pacbio sublong Rsubread
14 months ago thomas.heigl.ibk • 0
0
votes
0
replies
302
views
when FOLD>0, which group of sampls increased?
BASiCS
14 months ago Jeffcgen2000 • 0
0
votes
0
replies
301
views
Paired splsda
mixOmics
14 months ago michelafrancesconi8 • 0
0
votes
0
replies
633
views
Background normalization of Diffbind dba.normalize
Normalization DiffBind
14 months ago Young Boqin • 0
0
votes
0
replies
458
views
DMRcate pcutoff setting
EpicV2 DMRcate
14 months ago kitzhu • 0
0
votes
0
replies
454
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
14 months ago Anke • 0
1
vote
1
reply
986
views
WGCNA
DEGselection RNASeqData WGCNA
updated 14 months ago by ▴ 760 • written 14 months ago by • 0
0
votes
1
reply
470
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel ChIPQC
written 14 months ago by • 0
2
votes
8
replies
1.9k
views
miRTarRnaseq library
miRNATarget mirTarRnaSeq
updated 12 months ago by ▴ 20 • written 21 months ago by • 0
0
votes
1
reply
681
views
Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage Gviz sashimi
updated 6 months ago by • 0 • written 14 months ago by • 0
1
vote
1
reply
705
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
1
reply
998
views
Convert HGVS Representation back to Reference Genome Coordinates
GA4GHclient
updated 14 months ago by ▴ 160 • written 14 months ago by ★ 1.6k
0
votes
0
replies
476
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
14 months ago tim.meese • 0
0
votes
1
reply
827
views
BiomaRt - improved access to Ensembl ?
biomaRt
updated 14 months ago by ★ 6.6k • written 14 months ago by • 0
0
votes
0
replies
353
views
Deprecated Gates- tailgate
openCyto
14 months ago ztflaten • 0
0
votes
0
replies
390
views
Getting error while running GenomicPlot
GenomicPlot
14 months ago Lucky • 0
0
votes
0
replies
610
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
14 months ago Fernanda • 0
0
votes
0
replies
446
views
package rpx, unable to download any dataset (PRIDE, MassIVE, iProX)
rpx PXDataset RforProteomics
14 months ago Jane_Huang • 0
0
votes
0
replies
682
views
Generating Boxplots for Gene Expression by CellType in NanoStringGeoMXSet
GeomxTools SpatialDecon GeoMxWorkflows
14 months ago Cinque • 0
0
votes
0
replies
514
views
Trying to understand basic DiffBind usage
ChIPSeq DiffBind
15 months ago Alejandro • 0
0
votes
0
replies
900
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
15 months ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
646
views
Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
15 months ago Ragnhild • 0
0
votes
1
reply
1.4k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 14 months ago by ▴ 70 • written 15 months ago by • 0
0
votes
1
reply
633
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 15 months ago by ▴ 760 • written 15 months ago by • 0
0
votes
5
replies
1.2k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 14 months ago by ▴ 450 • written 15 months ago by • 0
0
votes
3
replies
865
views
concentration tables suitable as input for new packages?
Bioconductor
written 15 months ago by • 0
0
votes
1
reply
663
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
5
replies
1.6k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 14 months ago by ▴ 760 • written 15 months ago by • 0
0
votes
1
reply
626
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 15 months ago by 6.7k • written 15 months ago by • 0
0
votes
0
replies
693
views
Problem merging metadata and feature-table before analysing LEfSe on R
microbiomeDataSets differential-abundance
15 months ago 샤니쿠마리 • 0
2
votes
2
replies
1.2k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
15 months ago Assa Yeroslaviz ★ 1.5k
0
votes
2
replies
732
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 15 months ago by • 0
0
votes
0
replies
492
views
Z-score Interpretation across components
MAST
15 months ago GJ • 0
1
vote
2
replies
675
views
Review process for delivering R packages
Bioconductor
15 months ago XFWu • 0
0
votes
0
replies
548
views
BioCAsia 2024 Abstract Deadline - August 26th
BioCAsia2024 Community Conference Bioconductor
15 months ago Maria Doyle ▴ 110
0
votes
1
reply
739
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
15 months ago • updated 10 months ago Ian D. ▴ 70
1,000 results • Page 3 of 20
Recent ...
Replies
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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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
Awards • All
Popular Question to shepherl 4.2k
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Locations • All
WEHI, Melbourne, Australia, 5 minutes ago
Singapore, 27 minutes ago
The city by the bay, 30 minutes ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 2638 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6