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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 3 months ago by
s.malik
• 0 • written 14 months ago by
jenniewoo
▴ 70
5
votes
2
replies
682
views
outdated GEOmetadb.sqlite
GEOmetadb
14 months ago • updated 3 months ago
Robert Castelo
★ 3.3k
3
votes
1
reply
426
views
NPARC package y-variable
NPARC
NPA
updated 7 months ago by
nils.kurzawa
▴ 20 • written 7 months ago by
Aidan
• 0
3
votes
6
replies
270
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
23 days ago
nhaus
▴ 30
3
votes
3
replies
397
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 5 weeks ago by
alan.ocallaghan
▴ 160 • written 5 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
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
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
15
replies
695
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 11 weeks ago by
Michael Love
41k • written 12 weeks ago by
cinzia.spagnoli
• 0
2
votes
1
reply
508
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
6
replies
1.0k
views
Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
3 months ago • updated 10 weeks ago
Tobias
• 0
2
votes
2
replies
170
views
[DiffBind] Obtaining normalization factors
DiffBind
22 days ago • updated 18 days ago
Henry
▴ 10
2
votes
1
reply
211
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 5 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 weeks ago by
enee
▴ 10
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
514
views
Different genes expression with limma
DESeq2
DifferentialExpression
limma
updated 3 months ago by
Gordon Smyth
50k • written 4 months ago by
michelafrancesconi8
• 0
2
votes
2
replies
650
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
3 months ago
bd2000
▴ 30
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 11 weeks ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
2
votes
4
replies
609
views
BiocGenerics binary is outdated for macOS ARM
BiocGenerics
11 months ago
Michael Steinbaugh
▴ 90
2
votes
6
replies
397
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
26 days ago
Chris
• 0
2
votes
2
replies
311
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
10
replies
1.1k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago
rohitsatyam102
▴ 20
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
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
1.8k
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
469
views
Rbowtie2 problem
Rbowtie2
updated 4 months ago by
Dilara
• 0 • written 23 months ago by
Francisco
▴ 10
1
vote
1
reply
248
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
2
replies
611
views
Access genes associated with GO terms for a topGO object created with gene2GO
topGO
3 months ago
Dan
• 0
1
vote
2
replies
327
views
Inconsistent results in DiffBind
DiffBind
4 months ago
Sam
▴ 10
1
vote
3
replies
261
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
0
replies
438
views
Gviz : UcscTrack
rtracklayer
UCSC
Gviz
6 months ago
yujin
▴ 10
1
vote
0
replies
419
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet
subsetByOverlaps
GenomicInteractions
10 months ago
LaureTomas
▴ 10
1
vote
1
reply
354
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
Miquel
• 0
1
vote
11
replies
1.5k
views
BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
BiocParallel
updated 12 months ago by
Martin Morgan
25k • written 12 months ago by
Michael Steinbaugh
▴ 90
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
392
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 8 weeks ago by
Yang Liao
▴ 380 • written 3 months ago by
Joe Marturano
▴ 10
1
vote
1
reply
385
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
6 months ago
NiKo
▴ 10
1
vote
5
replies
343
views
fgsea fork
fgsea
updated 5 weeks ago by
James W. MacDonald
65k • written 5 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
10 months ago
Jiyoung Lee
• 0
1
vote
2
replies
713
views
gds in GEOmetadb 2023-06-26 version is empty
GEOmetadb
written 10 months ago by
malat1_t
▴ 10
1
vote
0
replies
174
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
9 weeks ago
BioinfoMug
• 0
1
vote
1
reply
380
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
467
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
12 weeks ago
mikat
• 0
1
vote
2
replies
287
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
3
replies
274
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 5 weeks ago by
mercedeh.movassagh
▴ 10 • written 6 weeks ago by
María
• 0
1
vote
2
replies
668
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
452
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
260
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 5 weeks ago by
SamGG
▴ 350 • written 11 weeks ago by
jarod
▴ 30
1
vote
2
replies
797
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
1
vote
4
replies
290
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
6 weeks ago
samuel.channon
• 0
394 results • Page
1 of 8
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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