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0
votes
1
reply
742
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DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
16 months ago • updated 10 months ago
Ian D.
▴ 70
0
votes
1
reply
957
views
installing "org.Hs.eg.db",go error
org.Hs.eg.db
updated 16 months ago by
shepherl
4.2k • written 16 months ago by
聪
• 0
0
votes
0
replies
505
views
Are equal whisker lengths important in an RLE plot?
EDASeq
EDA
16 months ago
BioinfGuru
▴ 70
0
votes
2
replies
1.0k
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 16 months ago by
nrenke
• 0 • written 16 months ago by
Lucie
• 0
0
votes
2
replies
971
views
FlowSOM library requires igraph but igraph does not install
FlowSOM
updated 7 months ago by
Szabolcs
• 0 • written 16 months ago by
Priyanka
• 0
0
votes
0
replies
559
views
hichip fragments extraction chip seq
ChIPSeqData
interact
GenomicRanges
HiC
16 months ago
user_bioinfo
• 0
0
votes
1
reply
630
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
16 months ago
mdidish
▴ 10
0
votes
0
replies
536
views
DiffBind dba.plotprofile y-axis range
DiffBind
16 months ago
Tara
• 0
0
votes
0
replies
475
views
proActiv-promoter analysis
proActiv
Transcriptomics
16 months ago
wang.xiangyu
• 0
0
votes
3
replies
716
views
How to combine multiple lists of cytoframes/cytocq data objects into one
flowWorkspace
cytocq
updated 16 months ago by
SamGG
▴ 360 • written 16 months ago by
anders.tondell
▴ 30
0
votes
0
replies
568
views
EuroBioC2024 Flashtalks & Birds-of-a-Feather Sessions - submissions open!
Community
Conference
Bioconductor
EuroBioC2024
16 months ago
Maria Doyle
▴ 110
0
votes
4
replies
994
views
Failed to install geneLenDataBase
geneLenDataBase
ChAMP
updated 16 months ago by
shepherl
4.2k • written 16 months ago by
Fang
• 0
4
votes
4
replies
1.8k
views
NAs in fgseaMultilevel
fgsea
updated 16 months ago by
alserg
▴ 280 • written 16 months ago by
Danté
• 0
0
votes
8
replies
1.4k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 16 months ago by
Rory Stark
★ 5.2k • written 16 months ago by
Marianna
▴ 20
0
votes
2
replies
1.8k
views
save.rnb.set warnings when trying to save rnb.set
RnBeads
RnBeads.hg19
MethylationArray
updated 6 months ago by
juansmurphy
• 0 • written 17 months ago by
hayleyw
• 0
0
votes
1
reply
702
views
Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment
seqFISH
SpatialExperiment
16 months ago
Matthew Thornton
▴ 390
0
votes
3
replies
1.9k
views
How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
gviz
Saccharomyces_cerevisiae
Gviz
ideogram
updated 16 months ago by
Maryna
• 0 • written 2.3 years ago by
Michael
• 0
0
votes
0
replies
612
views
Sigmatrix should not contain missing values error in deconvolution using granule
granulator
16 months ago
louis.der.hammer
• 0
0
votes
0
replies
667
views
Error in serialization
scDblFinder
BiocParallel
16 months ago
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
752
views
Retrieving Package Metadata from Bioconductor API: Versions and Dependencies
metaMSdata
updated 16 months ago by
shepherl
4.2k • written 16 months ago by
Sadman
• 0
0
votes
0
replies
667
views
Using variantAnnotation to put together genotype and consequence information
variantAnn
VariantAnnotation
17 months ago
ramiro.barrantes
▴ 10
0
votes
0
replies
466
views
ASICS to process NMR spectra
ASICS
17 months ago
KONG ZHI XIAN
• 0
0
votes
0
replies
540
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
17 months ago
Kelly
• 0
4
votes
9
replies
2.1k
views
Get_interactions is giving the combined score
STRINGdb
updated 16 months ago by
McKayl
• 0 • written 17 months ago by
nkavabhrath03
▴ 20
0
votes
0
replies
605
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
17 months ago
cereyredondo
• 0
0
votes
1
reply
612
views
output from RAIN doesn't look rhythmic
rain
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
cereyredondo
• 0
0
votes
0
replies
814
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer
MAST
DifferentialExpression
17 months ago
nhaus
▴ 70
3
votes
4
replies
1.3k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
17 months ago
jcollier
• 0
0
votes
1
reply
947
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
updated 12 months ago by
nereaherrera23
• 0 • written 17 months ago by
Mathu
• 0
1
vote
0
replies
624
views
RUVg spike-in assumption global expression
RUVSeq
RUVnormalize
17 months ago
Erdi
▴ 10
0
votes
0
replies
5
views
Spam:
Ground Handling Companies in Maldives
alabaster.schemas
db0
17 months ago
vvipflight01
0
0
votes
0
replies
11
views
Spam:
How do professional SEO services enhance user experience on my website?
metaMSdata
17 months ago
Steven
0
0
votes
0
replies
477
views
How to perform a methylation analyisis from beta values matrix and pd.csv
minfiDataEPIC
17 months ago
yemeijie123
• 0
0
votes
0
replies
433
views
Error in bam loading in getUniqueCleavageEvents() in GUIDEseq package
GUIDEseq
17 months ago
StayM
• 0
0
votes
0
replies
41
views
Spam:
GenOMICC DNA biobank
alabaster.schemas
db0
17 months ago
Jolka
0
0
votes
0
replies
515
views
EPIC v2 annotation and BigWig
EPICv2manifest
IlluminaHumanMethylationEPICv2anno.20a1.hg38
17 months ago
MajaVu
• 0
0
votes
0
replies
748
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq
AnnotationDbi
org.Hs.eg.db
17 months ago
chunglee13
• 0
0
votes
4
replies
1.9k
views
Trouble Installing DADA2 (warning: R new user)
dada2
updated 17 months ago by
shepherl
4.2k • written 17 months ago by
schott01
• 0
0
votes
0
replies
734
views
Difference in Predictive component of PLS and OPLS Model
Metabolomics
plotGrouper
Bioconductor
ropls
PLSDAbatch
17 months ago
devarti.mahakalkar
• 0
0
votes
0
replies
734
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi
EPICv2manifest
MethylAid
17 months ago
pcibin
• 0
0
votes
3
replies
975
views
Conumee with EPICv2 Segment function
Conu
conumee
updated 9 months ago by
zpingfeng
• 0 • written 17 months ago by
idatta1
• 0
0
votes
1
reply
708
views
single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 17 months ago by
Basti
▴ 780 • written 17 months ago by
tahirah.yasmin2014
• 0
1
vote
2
replies
794
views
How to get the DMR?
ENmix
17 months ago
Alex
• 0
0
votes
0
replies
397
views
Remove Control Probes from Affymetrix Human Gene 1.0 ST Array probeset version
AffymetrixDataTestFiles
AffymetrixChip
17 months ago
drexjaramel
• 0
0
votes
3
replies
1.0k
views
How to search Pubmed Central or other fulltext literature base using regex?
metaMSdata
Bioconductor
17 months ago
Abiologist
• 0
0
votes
0
replies
505
views
Understanding Differentially Abundant Neighbourhood Identification
miloR
17 months ago
Dario Strbenac
★ 1.6k
0
votes
2
replies
1.2k
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics
dada2
MicrobiomeData
17 months ago • updated 15 months ago
abhisek001
• 0
3
votes
1
reply
2.1k
views
Difference between enrichGO results and Enrichr website results
Pathways
GO.db
clusterProfiler
updated 17 months ago by
Guido Hooiveld
★ 4.1k • written 17 months ago by
adrip
▴ 10
0
votes
0
replies
725
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution
rnaseqGene
RNAseq
17 months ago
JG13
• 0
0
votes
0
replies
820
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
17 months ago
gamma.jian
▴ 10
1,000 results • Page
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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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