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Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
23 months ago • updated 22 months ago
Tobias
• 0
3
votes
2
replies
840
views
Question about DMRcate
DMRcate
dmrcate
23 months ago
chuanjiao6
• 0
1
vote
1
reply
1.0k
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 23 months ago by
alan.ocallaghan
▴ 160 • written 23 months ago by
Dario Strbenac
★ 1.6k
0
votes
2
replies
903
views
Cross-species analysis using DESeq2 - size factor computation
dese
DESeq2
23 months ago
pl23
• 0
6
votes
7
replies
1.3k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 23 months ago by
Gordon Smyth
53k • written 23 months ago by
aa.machado001
• 0
0
votes
2
replies
864
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus
RNASeqData
23 months ago
Diana
• 0
0
votes
1
reply
700
views
Annotatr Duplicate Entries
annotatr
AnnotationHub
written 23 months ago by
hayleyw
• 0
0
votes
0
replies
473
views
IlluminaHumanMethylation27kanno.ilmn12.hg19 package is mapped to hg18 genome
IlluminaHumanMethylation27kanno.ilmn12.hg19
23 months ago
Basti
▴ 780
2
votes
2
replies
765
views
News:
"Edit" button not working
Bioconductor
Website
SupportSite
written 24 months ago by
shepherl
4.2k
0
votes
0
replies
446
views
iSEE Difference Panel Missing
iSEEu
23 months ago
Dario Strbenac
★ 1.6k
1
vote
3
replies
1.2k
views
Big differences between biological replicates makes DESeq2 result 0
chipseq
DifferentialMethylation
DESeq2
updated 23 months ago by
Michael Love
43k • written 23 months ago by
rebw25
• 0
1
vote
3
replies
1.4k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 23 months ago by
georgii.vdovin
• 0
4
votes
1
reply
1.9k
views
When should I correct for batch effects
BatchEffect
SingleCellExperiment
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
NeuroDaniel
▴ 20
0
votes
2
replies
2.0k
views
Regressing out covariates from expression matrix for PCA visualization - can I use coefficients calculated in DESeq2??
DESeq2
23 months ago
tombate94
• 0
1
vote
8
replies
1.6k
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 23 months ago by
Gordon Smyth
53k • written 23 months ago by
sat
• 0
0
votes
1
reply
1.1k
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
23 months ago
isaromero8888
• 0
0
votes
1
reply
1.5k
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Max
• 0
0
votes
0
replies
781
views
News:
2024 May Institute on computation and statistics for mass spectrometry and proteomics
MSstats
MSstatsTMT
MSstatsShiny
MSstatsPTM
23 months ago
kohler.d
• 0
0
votes
3
replies
1.0k
views
Interaction tests and paired interaction tests in swish
swish
salmon
fishpond
updated 23 months ago by
Michael Love
43k • written 23 months ago by
Nicholas
• 0
0
votes
1
reply
692
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 23 months ago by
Ram
▴ 220 • written 23 months ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
1.0k
views
visualizing GSEA showCategory question
enrichplot
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Grace.Ciabattoni
• 0
0
votes
1
reply
1.2k
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 23 months ago by
ATpoint
★ 5.0k • written 23 months ago by
Ömür Koray
• 0
0
votes
2
replies
963
views
TCGA-GBM subtype tumor
curatedTCGAData
updated 23 months ago by
Marcel Ramos
700 • written 23 months ago by
vicmonm5
• 0
0
votes
0
replies
621
views
clusterSweep Warning k Capped
bluster
23 months ago
Dario Strbenac
★ 1.6k
0
votes
1
reply
750
views
Dimensionality reduction visualization
imcRtools
SingleCellData
imcdatasets
SpatialWorkflow
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Simon
• 0
1
vote
2
replies
1.2k
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
23 months ago
mirjanakessler
• 0
0
votes
0
replies
984
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
23 months ago
Jawahar
• 0
2
votes
4
replies
2.5k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
23 months ago
Sabiha
▴ 20
0
votes
2
replies
872
views
Which fasta files to use for tximeta makeLinkTxome
tximeta
DESeq2
23 months ago
JING
• 0
5
votes
6
replies
1.6k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
23 months ago
Shaimaa Gamal
• 0
0
votes
1
reply
550
views
DESEQ2 reduced model input into Pathfindr
DESeq2
updated 23 months ago by
Michael Love
43k • written 24 months ago by
a.raftery.1
• 0
0
votes
1
reply
800
views
Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2
timecourse
time
updated 23 months ago by
Michael Love
43k • written 24 months ago by
Anastasiia
• 0
2
votes
2
replies
1.1k
views
Deleting a column from data frame and then running DESeq2
DESeq2
updated 23 months ago by
Michael Love
43k • written 24 months ago by
amv112
▴ 10
0
votes
2
replies
2.0k
views
Plotting mean TPM of an expressed gene
DESeq2
24 months ago • updated 23 months ago
mp52226
• 0
0
votes
1
reply
904
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA
DESeq2
updated 23 months ago by
Michael Love
43k • written 24 months ago by
manuel
• 0
4
votes
6
replies
1.6k
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
24 months ago
Dario Strbenac
★ 1.6k
0
votes
3
replies
1.4k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 24 months ago by
Gordon Smyth
53k • written 24 months ago by
annasoudi
• 0
0
votes
0
replies
550
views
How to search for a string in a DNAStringSet dataset?
Biostrings
24 months ago
Angela Michalichyn
• 0
0
votes
0
replies
553
views
rpk per cell saved in SCE object.
SingleCellExperiment
24 months ago
JalapenoCornbread
• 0
0
votes
0
replies
625
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
24 months ago
frueher
• 0
3
votes
3
replies
2.0k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 24 months ago by
Gordon Smyth
53k • written 24 months ago by
Jurgen
• 0
2
votes
17
replies
4.5k
views
Problem installing package, version of dependency issue
AnnotationDbi
GO.db
updated 24 months ago by
Lluís Revilla Sancho
▴ 760 • written 24 months ago by
alexandre.blais
▴ 50
0
votes
1
reply
626
views
[DESEQ2] When to average biological replicates for hierarchical clustering
DESeq2
updated 24 months ago by
James W. MacDonald
68k • written 24 months ago by
E
• 0
2
votes
2
replies
637
views
How to interpret log2fold values when using numeric contrasts in DESEQ2?
DESeq2
24 months ago
pl23
• 0
1
vote
1
reply
2.2k
views
Error with biomaRt
biomaRt
updated 24 months ago by
Mike Smith
★ 6.6k • written 24 months ago by
goldenboy
• 0
2
votes
2
replies
800
views
How to contact Bioconductor's test host?
Bioconductor
updated 24 months ago by
Hervé Pagès
16k • written 24 months ago by
Marek Gierlinski
▴ 30
4
votes
2
replies
1.4k
views
Enrichement with clusterProfiler and biomart
biomaRt
clusterProfiler
Zea_mays
updated 24 months ago by
Guido Hooiveld
★ 4.1k • written 24 months ago by
sansan
• 0
1
vote
3
replies
908
views
makeOrgPackageFromNCBI generates an empty database?
OrganismDbi
makeOrgPackageFromNCBI
updated 24 months ago by
James W. MacDonald
68k • written 24 months ago by
dissikratzl
• 0
2
votes
2
replies
1.6k
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
24 months ago
bd2000
▴ 30
0
votes
4
replies
2.9k
views
Bioconductor installation
Bioconductor
written 2.0 years ago by
Akhil
• 0
46,710 results • Page
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Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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