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DEP
•
reset
2
votes
8
replies
1.7k
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
4.4 years ago
Wuschel
▴ 10
3
votes
7
replies
3.3k
views
Error when loading DEP in RStudio
dep
updated 2.9 years ago by
Desiree.
▴ 10 • written 3.2 years ago by
hele7
▴ 20
0
votes
7
replies
3.0k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 16 months ago by
Malcolm Cook
★ 1.6k • written 21 months ago by
Tobias
▴ 40
1
vote
7
replies
2.8k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData
Proteome
Database
DEP
2.7 years ago
tpm
• 0
1
vote
6
replies
2.9k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 3.4 years ago by
Laurent Gatto
1.6k • written 3.4 years ago by
jp
• 0
0
votes
4
replies
938
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
2.7 years ago
rina
▴ 30
1
vote
4
replies
1.3k
views
Failing to install DEP package. Some strange error.
R
Bioconductor
Install
DEP
2.7 years ago
tpm
• 0
0
votes
3
replies
3.8k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio
DEP
updated 2.7 years ago by
daniela.fuller
• 0 • written 2.9 years ago by
Tomaž
• 0
2
votes
3
replies
1.9k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute
missing value imputation
DEP
massspectrometry
updated 6.0 years ago by
Laurent Gatto
1.6k • written 6.0 years ago by
serpalma.v
▴ 60
3
votes
3
replies
983
views
Clarification of results tables in DEP
DEP
proteomics
updated 4.4 years ago by
arne.smits
▴ 70 • written 4.4 years ago by
António Miguel de Jesus Domingues
▴ 490
2
votes
3
replies
1.1k
views
DEP package: error in plot_heatmap
DEP
updated 4.3 years ago by
arne.smits
▴ 70 • written 4.3 years ago by
Rob
• 0
3
votes
3
replies
778
views
se does not inherit from class SummarizedExperiment
DEP
3.1 years ago
yueli7
▴ 20
1
vote
3
replies
1.2k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 2.6 years ago by
Basti
▴ 740 • written 2.6 years ago by
julie.hibbert
• 0
1
vote
2
replies
390
views
Error running run_app('LFQ')
LFQ
DEPpackage
run_app('LFQ')
ShinyApps
DEP
updated 4 months ago by
Ram
▴ 180 • written 5 months ago by
d.kozhevnikova
▴ 10
3
votes
2
replies
1.3k
views
DEP: Grouping Samples for missing value imputation
DEP
missing value imputation
proteomics
rforproteomics
6.0 years ago • updated 5.8 years ago
alex.gos90
▴ 10
0
votes
2
replies
412
views
Error message trying to open downloaded package
error
DEP
9 months ago
kcpaul168
• 0
1
vote
2
replies
1.6k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep
proteomics
limma
3.9 years ago
Rob
• 0
7
votes
2
replies
1.6k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 2.4 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 3.0 years ago by
Alexei Leliavski
▴ 60
0
votes
1
reply
458
views
Issue installing DEP package
DEP
updated 16 months ago by
shepherl
3.6k • written 16 months ago by
dheeraj.raya
• 0
0
votes
1
reply
667
views
I am using the DEP package example dataset, and I am getting this error on: plot_frequency(data_se)
DEP
R
Bioconductor
Plot
updated 3.0 years ago by
shepherl
3.6k • written 3.1 years ago by
tpm
• 0
1
vote
1
reply
673
views
DEP p.val adjustment
DEP
P.vals
adjustment
updated 4.7 years ago by
James W. MacDonald
64k • written 4.7 years ago by
826599
▴ 10
1
vote
1
reply
731
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.2 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 3.2 years ago by
justindean9208
▴ 10
0
votes
1
reply
900
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 8 months ago by
Simran
• 0 • written 2.6 years ago by
hele7
▴ 20
0
votes
1
reply
696
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 2.3 years ago by
James W. MacDonald
64k • written 2.3 years ago by
pedarf
• 0
0
votes
1
reply
929
views
How to remove batch effect on DEP protemics package?
Proteomics
DEP
MassSpectrometryData
updated 2.4 years ago by
bigomics.team
• 0 • written 2.4 years ago by
barrypraveen
• 0
0
votes
1
reply
304
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 8 months ago by
Basti
▴ 740 • written 8 months ago by
fuqichen1
• 0
0
votes
1
reply
617
views
Error in generating heatmap
dep
updated 3.5 years ago by
Kevin Blighe
3.9k • written 3.5 years ago by
nkvnambiar
• 0
0
votes
0
replies
664
views
Introduction to DEP - data imputation
DEP
impute
2.3 years ago
catherine.li
• 0
0
votes
0
replies
1.5k
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
written 2.4 years ago by
barrypraveen
• 0
0
votes
0
replies
817
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
4.2 years ago
dparrine
• 0
0
votes
0
replies
855
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
4.3 years ago
tatabox
• 0
0
votes
0
replies
680
views
DEP package - Understanding the results table
dep
proteomics
logFC
4.2 years ago
rina
▴ 30
0
votes
0
replies
656
views
How to obtain log2 intensity per sample in DEP?
DEP
2.5 years ago
hele7
▴ 20
0
votes
0
replies
322
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
7 months ago
aymanreffai
• 0
0
votes
0
replies
716
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
2.3 years ago
barrypraveen
• 0
0
votes
0
replies
527
views
Which package I can use?
MSnbase
DAPAR
DEP
3.1 years ago
yueli7
▴ 20
36 results • Page
1 of 1
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Comment: Java error while running HiCDC overview code
by
Joy
• 0
Thrilling, reminiscent are the emotions when playing the game Headle, a great game that helps you regain energy after a long, tiring, busy …
Comment: DiffBind getting Fold values of near 0
by
ATpoint
★ 3.6k
Almost certainly data are noisy and DESeq2 (which is used internally) shrinks the fold changes towards zero, because the naive fold changes…
Comment: metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
by
liqiong464
• 0
Hey, I encountered similiar problems now as handibles metentioned. But it seems a bit different somehow. I have 51 samples divided…
Comment: bam or VCF files from GSE75010
by
3
• 0
Because it is so clever and unique, I believe that many more ideas will be inspired by and borrowed from your original concept. [five night…
Comment: How does Deseq2 deal with the row with zero when calculating size factors
by
3
• 0
Thank you for sharing. I've read a great deal on relevant topics! Unlike other articles, yours really made an impression on me. I hope you'…
Votes
Comment: Ensembl down???
Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and
Comment: Ensembl down???
Answer: SingleR annotation of several slots/patients
Answer: List of Deprecated Packages for Bioc3.18
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Henrik Bengtsson
★ 2.4k
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to
paul.johnston
▴ 10
Teacher
to
Mike Smith
★ 6.2k
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to
Bine
▴ 20
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Robert Castelo
★ 3.0k
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