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Mass spec intensity difference
xcms
10 minutes ago
Phytochem
• 0
0
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0
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10
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DESeq2 for TRAP-seq methods
DESeq2
TRAP-seq
8 hours ago
marypiper
• 0
0
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0
replies
11
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Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
9 hours ago
Thomas.H.Hampton
• 0
0
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0
replies
16
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GenomeInfoDb’ could not be loaded or installed
GenomeInfoDbData
12 hours ago
ettore64
• 0
0
votes
1
reply
31
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Extract data from pair files
nimblegen
pair
updated 13 hours ago by
James W. MacDonald
56k • written 20 hours ago by
Dhanya
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0
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0
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18
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News:
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Bioconductor
13 hours ago
shepherl
2.6k
2
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3
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49
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Which DESeq normalization method?
DESeq2
updated 12 hours ago by
Michael Love
32k • written 14 hours ago by
save
• 0
0
votes
2
replies
48
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Error running ExperimentHubData::makeExperimentHubMetadata on Windows 10
BiocCheck
updated 14 hours ago by
shepherl
2.6k • written 2 days ago by
wewolski
▴ 10
1
vote
2
replies
69
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Failed to load "org.Mm.eg.db" package
org.Mm.eg.db
updated 16 hours ago by
shepherl
2.6k • written 4 days ago by
Nicol
• 0
4
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4
replies
101
views
How to apply limma-trend or voom to batch corrected single cell data? (non-integer and negative values included)
MNNCorrect
scMerge
limma-trend
4 days ago • updated 4 hours ago
hainct
• 0
0
votes
1
reply
47
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Correcting partially penetrant batch effect
DESeq2
updated 1 day ago by
Michael Love
32k • written 2 days ago by
swbarnes2
▴ 680
2
votes
1
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50
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tximeta Error in UseMethod("filter_")
tximeta
updated 1 day ago by
Michael Love
32k • written 1 day ago by
Pufall, Miles A
▴ 30
3
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2
replies
75
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Error Loading "org.Dm.eg.db" package
r
org.Dm.eg.db
updated 1 day ago by
Chris Seidel
▴ 70 • written 1 day ago by
Amanda
▴ 10
3
votes
2
replies
47
views
Complex Heatmap shows just one color
Heatmap
ComplexHeatmap
colorRamp
1 day ago
Assa Yeroslaviz
★ 1.5k
39
votes
28
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2.4k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 15 hours ago by
konglingmingklm
• 0 • written 8 days ago by
Arun
▴ 150
0
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0
replies
26
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PCA theoretical question for applied case
pcaMethods
1 day ago
Gero
• 0
0
votes
1
reply
80
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Error: package or namespace load failed for ‘org.Hs.eg.db’:
$operator
atomicvectors
updated 2 days ago by
James W. MacDonald
56k • written 2 days ago by
dazhiruoyujingjie
• 0
2
votes
2
replies
136
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Error: package or namespace load failed for ‘org.Mm.eg.db':
org.Mm.eg.db
2 days ago
Jack
• 0
0
votes
0
replies
23
views
motifBreakR error with custom BSgenome and snps.from.file function
GenomeInfoDb
motifbreakR
2 days ago
Chris Seidel
▴ 70
0
votes
11
replies
218
views
Aspli: error with gbCounts
Aspli
ASpli
written 28 days ago by
jbono
• 0
1
vote
1
reply
46
views
plotMA difference using or not a sub matrix
matrixsubset
DESeq2
plotMA
updated 3 days ago by
Michael Love
32k • written 4 days ago by
l.troxler
▴ 10
1
vote
8
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129
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DESeq problems
help
DESeq2
DESeqDataSetFromMatrix
rownames
updated 1 day ago by
Kevin Blighe
2.8k • written 4 days ago by
dorina.jamniczky
• 0
0
votes
9
replies
611
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Thoughts on computer purchase
computer
updated 3 days ago by
Gordon Smyth
42k • written 15.0 years ago by
Lance Palmer
▴ 60
2
votes
2
replies
80
views
Error following instructions of CBioportal R-workshop example 2
MultiAssayExperiment
cBioPortalData
updated 1 day ago by
Kevin Blighe
2.8k • written 4 days ago by
Javier
• 0
0
votes
1
reply
23
views
ChIPQC error in previously working code (BAM association error)
chipqc
updated 3 days ago by
Anaysha
• 0 • written 4 days ago by
cviner
• 0
0
votes
6
replies
112
views
Sample quality weights for RNA-seq
DESeq2
limma
weight
5 days ago • updated 2 days ago
Naomi Altman
★ 6.0k
1
vote
2
replies
127
views
CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
14 days ago • updated 9 hours ago
mwong043
• 0
1
vote
2
replies
53
views
Warning with the example of GSEA
fgsea
fgse
updated 4 days ago by
Kevin Blighe
2.8k • written 4 days ago by
julie.hardy
• 0
3
votes
2
replies
40
views
Biomart Errors
biomaRt
4 days ago
Dr. Connie Brett
▴ 10
0
votes
2
replies
90
views
DepMap copy number
software error
depmap
updated 1 day ago by
E
• 0 • written 6 months ago by
DannyM
• 0
0
votes
1
reply
40
views
High fold change reported for comparison of samples with zero values in all samples
edgeR
updated 4 days ago by
James W. MacDonald
56k • written 4 days ago by
Laura
• 0
0
votes
1
reply
39
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 4 days ago by
Mike Smith
★ 4.9k • written 4 days ago by
Jeremy
• 0
2
votes
1
reply
35
views
Warning in EnhancedVolcano plot
volcano-plot
EnhancedVolcano
updated 4 days ago by
Kevin Blighe
2.8k • written 4 days ago by
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
64
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
4 days ago • updated 14 hours ago
xiaofeiwang18266
▴ 20
0
votes
0
replies
16
views
layout has more positions than samples but omixerRand doesn't randomize the samples
Omixer
4 days ago
Lluís Revilla Sancho
▴ 630
0
votes
1
reply
42
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3 days ago by
Sam
▴ 10 • written 5 days ago by
ikumar2000
• 0
1
vote
15
replies
195
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
6 days ago • updated 3 days ago
demisa
• 0
1
vote
4
replies
72
views
EnhancedVolcano plot with colCustom
EnhancedVolcano
5 days ago • updated 8 hours ago
Neeraja Vegesna
▴ 10
0
votes
2
replies
86
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db
Transcriptomics
5 days ago
Kate
• 0
1
vote
1
reply
46
views
Enhanced Volcano Plot Controlling Color Layers
EnhancedVolcano
5 days ago
dk0319
• 0
4
votes
2
replies
72
views
TargetsFile. Where it is?
Limma
ArrayExpress
GEO
updated 5 days ago by
James W. MacDonald
56k • written 5 days ago by
Gero
• 0
0
votes
0
replies
28
views
Missing sample
OSAT
5 days ago
Lluís Revilla Sancho
▴ 630
0
votes
1
reply
54
views
Query regarding edgeR and limma
limma
readDGE
edgeR
updated 5 days ago by
James W. MacDonald
56k • written 6 days ago by
abhisekdey061
• 0
1
vote
0
replies
30
views
News:
Terra / AnVIL R / Bioconductor Popup Workshops
AnVIL
workshop
Bioconductor
Terra
5 days ago
shepherl
2.6k
0
votes
0
replies
24
views
News:
Bioconductor Release 3.12 and Bioconductor Devel 3.13 Code Freeze Deadlines!
deadline
Bioconductor
devel
release
5 days ago
shepherl
2.6k
0
votes
0
replies
32
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
5 days ago
hele7
▴ 20
0
votes
0
replies
32
views
Job:
Biostatistics Research Associate, York, UK
QTL
fourier
TimeSeriesExperiment
timecoursedata
5 days ago
Daphne
• 0
0
votes
0
replies
55
views
How can I get normalized counts with ImpulseDE2?
ImpulseDE2
5 days ago • updated 21 hours ago
MU
• 0
1
vote
1
reply
55
views
simplifyEnrichment install error
package
Rversion
Install
simplifyEnrichment
updated 5 days ago by
shepherl
2.6k • written 5 days ago by
ch_el
▴ 10
4
votes
14
replies
995
views
Couldn't load org.Hs.eg.db
org.Hs.eg.db
updated 13 hours ago by
Charlotte Soneson
▴ 130 • written 6 days ago by
Chen
▴ 20
40,578 results • Page
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Replies
Comment: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
by
hainct
• 0
Thank you @alun
Comment: EnhancedVolcano plot with colCustom
by
Neeraja Vegesna
▴ 10
Hi Kevin, It worked once I added `names(keyvals.colour1)[keyvals.colour1 == '#8F8F8F'] <- 'NA'`. ![volcanoplot][1] Thanks a lot for you…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza
by
mwong043
• 0
Thanks Rory. I tried the first method by defining a vector containing the normalisation factors for my samples and it worked. I am just wo…
Comment: EnhancedVolcano plot with colCustom
by
Kevin Blighe
2.8k
Hi, that's great that it works with a lower number of groups. Can you re-check the logic flow when you are using more groups? *EnhancedVolc…
Comment: EnhancedVolcano plot with colCustom
by
Neeraja Vegesna
▴ 10
Hi Kevin, When I run the function in my previous post, the only warning I get is the following.. > Warning message: One or more p-values …
Votes
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Comment: EnhancedVolcano plot with colCustom
Comment: Which DESeq normalization method?
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