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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
Michael Love
43k • written 13 months ago by
Alpesh Querer
▴ 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
Lluís Revilla Sancho
▴ 760 • written 14 months ago by
Nasim
• 0
0
votes
1
reply
470
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel
ChIPQC
written 14 months ago by
Young Boqin
• 0
2
votes
8
replies
1.9k
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 12 months ago by
mercedeh.movassagh
▴ 20 • written 21 months ago by
María Calvo
• 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
macdonaldfrench7286566
• 0 • written 14 months ago by
Marco
• 0
1
vote
1
reply
705
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
Pimpa
• 0
1
vote
1
reply
998
views
Convert HGVS Representation back to Reference Genome Coordinates
GA4GHclient
updated 14 months ago by
Vince Schulz
▴ 160 • written 14 months ago by
Dario Strbenac
★ 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
Mike Smith
★ 6.6k • written 14 months ago by
Abiologist
• 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
Aidan
▴ 70 • written 15 months ago by
semra
• 0
0
votes
1
reply
633
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 15 months ago by
Lluís Revilla Sancho
▴ 760 • written 15 months ago by
emilymily77
• 0
0
votes
5
replies
1.2k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 14 months ago by
Yang Liao
▴ 450 • written 15 months ago by
venusian.martin
• 0
0
votes
3
replies
865
views
concentration tables suitable as input for new packages?
Bioconductor
written 15 months ago by
katja.danielzik
• 0
0
votes
1
reply
663
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
bioinformaticssrm2011
• 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
Lluís Revilla Sancho
▴ 760 • written 15 months ago by
semra
• 0
0
votes
1
reply
626
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 15 months ago by
Vincent J. Carey, Jr.
6.7k • written 15 months ago by
kmzhou4
• 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
Shaimaa Gamal
• 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 ...
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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
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