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8
votes
7
replies
1.2k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 5 months ago by
Daniel E. Weeks
▴ 30
5
votes
1
reply
1.4k
views
Support for new Illumina human methylation EPIC array v2
human
methylationArrayAnalysis
updated 4 months ago by
s.malik
• 0 • written 14 months ago by
jenniewoo
▴ 70
5
votes
2
replies
694
views
outdated GEOmetadb.sqlite
GEOmetadb
15 months ago • updated 3 months ago
Robert Castelo
★ 3.3k
3
votes
6
replies
306
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
3
votes
1
reply
1.9k
views
TwoSampleMR and ieugwasr
ieugwasr
clumping
TwoSampleMR
updated 9 weeks ago by
zoheir.alayash
▴ 10 • written 2.2 years ago by
S T
▴ 90
3
votes
5
replies
1.2k
views
why is downloading the .tar.gz file for a given bioconductor package, then installing with R CMD INSTALL so much more effective than BiocManager::ins…
Bioconductor
Install
library
biocmanager
updated 10 months ago by
Vincent J. Carey, Jr.
6.7k • written 10 months ago by
Ndimensional
▴ 20
3
votes
1
reply
440
views
NPARC package y-variable
NPARC
NPA
updated 8 months ago by
nils.kurzawa
▴ 20 • written 8 months ago by
Aidan
• 0
3
votes
3
replies
456
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 7 weeks ago by
alan.ocallaghan
▴ 160 • written 7 weeks ago by
Najla Abassi
• 0
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib
rhdf5
3.2 years ago • updated 9 months ago
Thomas Sandmann
▴ 90
2
votes
1
reply
525
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 11 months ago by
andres.firrincieli
▴ 50 • written 11 months ago by
hesse.sebastian
▴ 10
2
votes
2
replies
331
views
How to contact Bioconductor's test host?
Bioconductor
updated 4 months ago by
Hervé Pagès
16k • written 4 months ago by
Marek Gierlinski
▴ 30
2
votes
6
replies
464
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
5 weeks ago
Chris
▴ 10
2
votes
15
replies
731
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 3 months ago by
Michael Love
42k • written 3 months ago by
cinzia.spagnoli
• 0
2
votes
2
replies
191
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago
Henry
▴ 10
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 3 months ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
2
votes
10
replies
1.2k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago
rohitsatyam102
▴ 20
2
votes
6
replies
1.1k
views
Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
3 months ago • updated 12 weeks ago
Tobias
• 0
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 3 months ago by
marcusn
• 0 • written 2.4 years ago by
bhanu.chandra1
• 0
2
votes
7
replies
381
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
10 days ago • updated 7 days ago
sajadahmad41454
• 0
2
votes
4
replies
549
views
Different genes expression with limma
DESeq2
DifferentialExpression
limma
updated 4 months ago by
Gordon Smyth
50k • written 5 months ago by
michelafrancesconi8
• 0
2
votes
2
replies
685
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
4 months ago
bd2000
▴ 30
2
votes
13
replies
481
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
27 days ago • updated 24 days ago
fernanda.backsouza
▴ 10
2
votes
4
replies
623
views
BiocGenerics binary is outdated for macOS ARM
BiocGenerics
11 months ago
Michael Steinbaugh
▴ 90
2
votes
1
reply
232
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 7 weeks ago by
Guido Hooiveld
★ 4.0k • written 8 weeks ago by
enee
▴ 10
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 4 months ago by
Guido Hooiveld
★ 4.0k • written 14 months ago by
ruiqi.li
▴ 10
2
votes
2
replies
2.4k
views
Biostatistician Position: UMass Medical School
Microarray
Microarray
written 16.8 years ago by
David Lapointe
▴ 190
1
vote
7
replies
1.9k
views
Error using champ.import
ChAMP
EPICv2
updated 4 weeks ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
1
vote
3
replies
271
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 8 weeks ago by
Marcel Ramos
700 • written 8 weeks ago by
Astrid Deschênes
• 0
1
vote
3
replies
1.6k
views
conumee with Infinium MethylationEPIC v2.0
MethylationEPICv2.0
conumee
updated 9 months ago by
sgomez
• 0 • written 14 months ago by
luca.s
▴ 50
1
vote
1
reply
413
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 10 weeks ago by
Yang Liao
▴ 380 • written 3 months ago by
Joe Marturano
▴ 10
1
vote
5
replies
484
views
BiomaRt download data error
biomaRt
updated 3 months ago by
Mike Smith
★ 6.5k • written 3 months ago by
Max Bone
• 0
1
vote
4
replies
1.8k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR
SeuratscRNA
written 5 months ago by
Bine
▴ 40
1
vote
1
reply
417
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
6 months ago
NiKo
▴ 10
1
vote
2
replies
180
views
Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago
Sherin
• 0
1
vote
5
replies
368
views
fgsea fork
fgsea
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
yimjohns
• 0
1
vote
4
replies
1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
11 months ago
Jiyoung Lee
• 0
1
vote
1
reply
271
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 7 weeks ago by
SamGG
▴ 350 • written 3 months ago by
jarod
▴ 30
1
vote
1
reply
266
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 3 months ago by
alan.ocallaghan
▴ 160 • written 3 months ago by
Dario Strbenac
★ 1.5k
1
vote
0
replies
445
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet
subsetByOverlaps
GenomicInteractions
10 months ago
LaureTomas
▴ 10
1
vote
1
reply
275
views
Minimum datasets needed for meta analysis
RnaSeqSampleSize
updated 5 months ago by
Basti
▴ 780 • written 5 months ago by
Durga
▴ 10
1
vote
1
reply
403
views
How to read fcs3.2 files
flowCore
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
Gabriel
▴ 10
1
vote
2
replies
350
views
Inconsistent results in DiffBind
DiffBind
5 months ago
Sam
▴ 10
1
vote
0
replies
189
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
11 weeks ago
BioinfoMug
• 0
1
vote
4
replies
504
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
3 months ago
mikat
• 0
1
vote
0
replies
251
views
Attempting to import SBML file using R
SBMLR
sbml
rsbm
rsbml
updated 5 months ago by
Michael Love
42k • written 5 months ago by
isasg
▴ 10
1
vote
2
replies
306
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 8 weeks ago by
ATpoint
★ 4.1k • written 8 weeks ago by
maximilian.beikirch
• 0
1
vote
3
replies
891
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 24 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
699
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
5 months ago • updated 4 months ago
Levi
• 0
1
vote
1
reply
478
views
Rbowtie2 problem
Rbowtie2
updated 4 months ago by
Dilara
• 0 • written 23 months ago by
Francisco
▴ 10
1
vote
0
replies
461
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics
DifferentialRegulation
limma
8 months ago
svlachavas
▴ 830
400 results • Page
1 of 8
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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