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8
votes
7
replies
1.2k
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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 3 months ago by
s.malik
• 0 • written 14 months ago by
jenniewoo
▴ 70
5
votes
2
replies
687
views
outdated GEOmetadb.sqlite
GEOmetadb
14 months ago • updated 3 months ago
Robert Castelo
★ 3.3k
3
votes
5
replies
1.1k
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 9 months ago by
Vincent J. Carey, Jr.
6.7k • written 9 months ago by
Ndimensional
▴ 20
3
votes
1
reply
430
views
NPARC package y-variable
NPARC
NPA
updated 7 months ago by
nils.kurzawa
▴ 20 • written 7 months ago by
Aidan
• 0
3
votes
3
replies
404
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 6 weeks ago by
alan.ocallaghan
▴ 160 • written 6 weeks ago by
Najla Abassi
• 0
3
votes
1
reply
1.8k
views
TwoSampleMR and ieugwasr
ieugwasr
clumping
TwoSampleMR
updated 7 weeks ago by
zoheir.alayash
▴ 10 • written 2.1 years ago by
S T
▴ 90
3
votes
6
replies
276
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
25 days ago
nhaus
▴ 30
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib
rhdf5
3.2 years ago • updated 8 months ago
Thomas Sandmann
▴ 90
2
votes
6
replies
404
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
28 days ago
Chris
• 0
2
votes
15
replies
702
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 12 weeks ago by
Michael Love
41k • written 12 weeks ago by
cinzia.spagnoli
• 0
2
votes
1
reply
511
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
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 12 weeks ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
24 days ago • updated 20 days ago
Henry
▴ 10
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 14 months ago by
ruiqi.li
▴ 10
2
votes
2
replies
655
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
3 months ago
bd2000
▴ 30
2
votes
10
replies
1.1k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago
rohitsatyam102
▴ 20
2
votes
2
replies
2.4k
views
Biostatistician Position: UMass Medical School
Microarray
Microarray
written 16.8 years ago by
David Lapointe
▴ 190
2
votes
4
replies
610
views
BiocGenerics binary is outdated for macOS ARM
BiocGenerics
11 months ago
Michael Steinbaugh
▴ 90
2
votes
2
replies
312
views
How to contact Bioconductor's test host?
Bioconductor
updated 3 months ago by
Hervé Pagès
16k • written 3 months ago by
Marek Gierlinski
▴ 30
2
votes
4
replies
520
views
Different genes expression with limma
DESeq2
DifferentialExpression
limma
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
michelafrancesconi8
• 0
2
votes
1
reply
213
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 6 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 weeks ago by
enee
▴ 10
2
votes
6
replies
1.0k
views
Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
3 months ago • updated 11 weeks ago
Tobias
• 0
2
votes
13
replies
417
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
15 days ago • updated 12 days ago
fernanda.backsouza
▴ 10
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 11 weeks ago by
marcusn
• 0 • written 2.4 years ago by
bhanu.chandra1
• 0
1
vote
3
replies
1.9k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 11 weeks ago by
cinzia.spagnoli
• 0 • written 23 months ago by
AP
• 0
1
vote
1
reply
470
views
Rbowtie2 problem
Rbowtie2
updated 4 months ago by
Dilara
• 0 • written 23 months ago by
Francisco
▴ 10
1
vote
3
replies
262
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 6 weeks ago by
Marcel Ramos
690 • written 6 weeks ago by
Astrid Deschênes
• 0
1
vote
5
replies
437
views
BiomaRt download data error
biomaRt
updated 12 weeks ago by
Mike Smith
★ 6.5k • written 3 months ago by
Max Bone
• 0
1
vote
3
replies
1.5k
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
394
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 9 weeks ago by
Yang Liao
▴ 380 • written 3 months ago by
Joe Marturano
▴ 10
1
vote
1
reply
389
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
6 months ago
NiKo
▴ 10
1
vote
5
replies
350
views
fgsea fork
fgsea
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
yimjohns
• 0
1
vote
1
reply
409
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by
tangming2005
▴ 190 • written 6 months ago by
meenae
▴ 10
1
vote
4
replies
1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
10 months ago
Jiyoung Lee
• 0
1
vote
1
reply
1.1k
views
Issue with lengthConnectors in EnhancedVolcano
EnhancedVolcano
updated 4 months ago by
mohamad.hajo89
• 0 • written 2.4 years ago by
ikotlar
▴ 10
1
vote
3
replies
866
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 12 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
717
views
gds in GEOmetadb 2023-06-26 version is empty
GEOmetadb
written 10 months ago by
malat1_t
▴ 10
1
vote
4
replies
295
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
6 weeks ago
samuel.channon
• 0
1
vote
1
reply
268
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
383
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
4
replies
473
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
3 months ago
mikat
• 0
1
vote
2
replies
291
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 6 weeks ago by
ATpoint
★ 4.1k • written 6 weeks ago by
maximilian.beikirch
• 0
1
vote
2
replies
220
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
18 days ago
Le
• 0
1
vote
1
reply
250
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
1
reply
1.3k
views
featureCounts running too long
RNAseq123
updated 3 months ago by
difraiadomenico
• 0 • written 3.2 years ago by
demirkalecy
▴ 10
1
vote
2
replies
673
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
5 months ago • updated 4 months ago
Levi
• 0
1
vote
0
replies
456
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics
DifferentialRegulation
limma
8 months ago
svlachavas
▴ 830
1
vote
1
reply
264
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 6 weeks ago by
SamGG
▴ 350 • written 11 weeks ago by
jarod
▴ 30
1
vote
2
replies
801
views
Error: biomaRt has encountered an unexpected server error.
biomaRt
updated 11 months ago by
Mike Smith
★ 6.5k • written 11 months ago by
Yijing
• 0
393 results • Page
1 of 8
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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