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0
votes
0
replies
267
views
Getting error while running GenomicPlot
GenomicPlot
6 months ago
Lucky
• 0
0
votes
0
replies
362
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
6 months ago
Fernanda
• 0
0
votes
0
replies
253
views
package rpx, unable to download any dataset (PRIDE, MassIVE, iProX)
rpx
PXDataset
RforProteomics
6 months ago
Jane_Huang
• 0
0
votes
0
replies
505
views
Generating Boxplots for Gene Expression by CellType in NanoStringGeoMXSet
GeomxTools
SpatialDecon
GeoMxWorkflows
6 months ago
Cinque
• 0
0
votes
0
replies
310
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
7 months ago
Alejandro
• 0
0
votes
0
replies
557
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel
scran
BiocParall
7 months ago
Lluís Revilla Sancho
▴ 760
0
votes
0
replies
394
views
Mark seleced variables in the x-loading plot
OPLS
genomes
Proteomics
7 months ago
Ragnhild
• 0
0
votes
1
reply
990
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings
packageinstallation
updated 7 months ago by
Aidan
▴ 60 • written 7 months ago by
semra
• 0
0
votes
1
reply
437
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 7 months ago by
Lluís Revilla Sancho
▴ 760 • written 7 months ago by
emilymily77
• 0
0
votes
5
replies
961
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 6 months ago by
Yang Liao
▴ 450 • written 7 months ago by
venusian.martin
• 0
0
votes
3
replies
657
views
concentration tables suitable as input for new packages?
Bioconductor
written 7 months ago by
katja.danielzik
• 0
0
votes
1
reply
457
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
bioinformaticssrm2011
• 0
0
votes
5
replies
1.1k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor
clusterProfiler
updated 6 months ago by
Lluís Revilla Sancho
▴ 760 • written 7 months ago by
semra
• 0
0
votes
1
reply
448
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 7 months ago by
Vincent J. Carey, Jr.
6.7k • written 7 months ago by
kmzhou4
• 0
0
votes
0
replies
509
views
Problem merging metadata and feature-table before analysing LEfSe on R
microbiomeDataSets
differential-abundance
7 months ago
샤니쿠마리
• 0
2
votes
2
replies
923
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
7 months ago
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
511
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion
ReactomeGSA
BatchEffect
written 7 months ago by
Shaimaa Gamal
• 0
0
votes
0
replies
393
views
Z-score Interpretation across components
MAST
7 months ago
GJ
• 0
1
vote
2
replies
494
views
Review process for delivering R packages
Bioconductor
7 months ago
XFWu
• 0
0
votes
0
replies
357
views
BioCAsia 2024 Abstract Deadline - August 26th
BioCAsia2024
Community
Conference
Bioconductor
7 months ago
Maria Doyle
▴ 100
0
votes
1
reply
532
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
8 months ago • updated 9 weeks ago
Ian D.
▴ 70
0
votes
1
reply
675
views
installing "org.Hs.eg.db",go error
org.Hs.eg.db
updated 8 months ago by
shepherl
4.1k • written 8 months ago by
聪
• 0
0
votes
0
replies
339
views
Are equal whisker lengths important in an RLE plot?
EDASeq
EDA
8 months ago
BioinfGuru
▴ 70
0
votes
2
replies
734
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 7 months ago by
nrenke
• 0 • written 8 months ago by
Lucie
• 0
0
votes
2
replies
449
views
FlowSOM library requires igraph but igraph does not install
FlowSOM
written 8 months ago by
Priyanka
• 0
0
votes
0
replies
350
views
hichip fragments extraction chip seq
ChIPSeqData
interact
GenomicRanges
HiC
8 months ago
user_bioinfo
• 0
0
votes
1
reply
402
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
8 months ago
mdidish
▴ 10
0
votes
0
replies
333
views
DiffBind dba.plotprofile y-axis range
DiffBind
8 months ago
Tara
• 0
0
votes
0
replies
320
views
proActiv-promoter analysis
proActiv
Transcriptomics
8 months ago
wang.xiangyu
• 0
0
votes
3
replies
463
views
How to combine multiple lists of cytoframes/cytocq data objects into one
flowWorkspace
cytocq
updated 8 months ago by
SamGG
▴ 360 • written 8 months ago by
anders.tondell
▴ 30
0
votes
0
replies
356
views
EuroBioC2024 Flashtalks & Birds-of-a-Feather Sessions - submissions open!
Community
Conference
Bioconductor
EuroBioC2024
8 months ago
Maria Doyle
▴ 100
0
votes
4
replies
667
views
Failed to install geneLenDataBase
geneLenDataBase
ChAMP
updated 8 months ago by
shepherl
4.1k • written 8 months ago by
Fang
• 0
4
votes
4
replies
1.3k
views
NAs in fgseaMultilevel
fgsea
updated 8 months ago by
alserg
▴ 280 • written 8 months ago by
Danté
• 0
0
votes
8
replies
953
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 8 months ago by
Rory Stark
★ 5.2k • written 8 months ago by
Marianna
▴ 20
0
votes
1
reply
504
views
Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment
seqFISH
SpatialExperiment
8 months ago
Matthew Thornton
▴ 380
0
votes
3
replies
1.7k
views
How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
gviz
Saccharomyces_cerevisiae
Gviz
ideogram
updated 8 months ago by
Maryna
• 0 • written 19 months ago by
Michael
• 0
0
votes
0
replies
483
views
Sigmatrix should not contain missing values error in deconvolution using granule
granulator
8 months ago
louis.der.hammer
• 0
0
votes
0
replies
486
views
Error in serialization
scDblFinder
BiocParallel
8 months ago
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
571
views
Retrieving Package Metadata from Bioconductor API: Versions and Dependencies
metaMSdata
updated 8 months ago by
shepherl
4.1k • written 8 months ago by
Sadman
• 0
0
votes
0
replies
504
views
Using variantAnnotation to put together genotype and consequence information
variantAnn
VariantAnnotation
8 months ago
ramiro.barrantes
▴ 10
0
votes
0
replies
338
views
ASICS to process NMR spectra
ASICS
9 months ago
KONG ZHI XIAN
• 0
0
votes
0
replies
373
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
9 months ago
Kelly
• 0
4
votes
9
replies
1.6k
views
Get_interactions is giving the combined score
STRINGdb
updated 8 months ago by
McKayl
• 0 • written 9 months ago by
nkavabhrath03
▴ 20
0
votes
0
replies
399
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
9 months ago
cereyredondo
• 0
0
votes
1
reply
457
views
output from RAIN doesn't look rhythmic
rain
updated 9 months ago by
ATpoint
★ 4.8k • written 9 months ago by
cereyredondo
• 0
0
votes
0
replies
590
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer
MAST
DifferentialExpression
9 months ago
nhaus
▴ 70
3
votes
4
replies
994
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
9 months ago
jcollier
• 0
0
votes
1
reply
705
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
updated 4 months ago by
nereaherrera23
• 0 • written 9 months ago by
Mathu
• 0
1
vote
0
replies
384
views
RUVg spike-in assumption global expression
RUVSeq
RUVnormalize
9 months ago
Erdi
▴ 10
0
votes
0
replies
5
views
Spam:
Ground Handling Companies in Maldives
alabaster.schemas
db0
9 months ago
vvipflight01
0
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Answer: Version conflict when pushing to scQTLtools devel branch
by
shepherl
4.1k
There is a Bioconductor release today. There were notifications on the bioc-devel mailing list https://stat.ethz.ch/pipermail/bioc-devel…
Comment: DiffBind can't find a DAR
by
Mengjun
• 0
The details about this question: I have 4 samples with 2 conditions( ctrl_1, ctrl_2, ko_1, ko_2), i use these 4 samples as input. Here is …
Comment: DiffBind can't find a DAR
by
Mengjun
• 0
Thank you very much for pointing out this shortcoming. I will improve it.
Comment: samtools loading in R
by
Charlie
• 0
This is obviously a very late answer but I had a similar error: > sh: samtools: command not found > > sh: samtools: command not found > …
Comment: Easiest way to convert read10xMolInfo data into a dataframe in R with gene label
by
njmcdirect
• 0
https://www.www-njmcdirect.run/
Votes
Comment: biomaRt server error, and mirrors do not help
Bioconductor 3.21 is Released!
DiffBind - question on the use of filtered or unfiltered input data
Answer: Enhanced Volcano Error when drawing connectors
Answer: Origin of the labels for the SingleCellMultiModal dataset
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