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DEP
•
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0
votes
0
replies
259
views
Warning while loading DEP package
DEP
updated 7 months ago by
shepherl
4.1k • written 7 months ago by
Namrata
• 0
0
votes
3
replies
719
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 9 months ago by
Gordon Smyth
52k • written 9 months ago by
Laura
• 0
1
vote
2
replies
952
views
Error running run_app('LFQ')
LFQ
DEPpackage
run_app('LFQ')
ShinyApps
DEP
updated 17 months ago by
Ram
▴ 220 • written 17 months ago by
d.kozhevnikova
▴ 10
0
votes
0
replies
678
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
20 months ago
aymanreffai
• 0
0
votes
1
reply
610
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 20 months ago by
Basti
▴ 780 • written 20 months ago by
fuqichen1
• 0
0
votes
2
replies
750
views
Error message trying to open downloaded package
error
DEP
22 months ago
kcpaul168
• 0
0
votes
1
reply
763
views
Issue installing DEP package
DEP
updated 2.3 years ago by
shepherl
4.1k • written 2.3 years ago by
dheeraj.raya
• 0
0
votes
7
replies
4.4k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 2.3 years ago by
Malcolm Cook
★ 1.6k • written 2.8 years ago by
Tobias
▴ 40
0
votes
0
replies
992
views
Introduction to DEP - data imputation
DEP
impute
3.3 years ago
catherine.li
• 0
0
votes
0
replies
1.1k
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
3.3 years ago
barrypraveen
• 0
0
votes
1
reply
1.0k
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 3.4 years ago by
James W. MacDonald
67k • written 3.4 years ago by
pedarf
• 0
0
votes
1
reply
1.4k
views
How to remove batch effect on DEP protemics package?
Proteomics
DEP
MassSpectrometryData
updated 3.4 years ago by
bigomics.team
• 0 • written 3.4 years ago by
barrypraveen
• 0
0
votes
0
replies
2.2k
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
written 3.4 years ago by
barrypraveen
• 0
0
votes
0
replies
1.1k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.5 years ago
hele7
▴ 20
1
vote
3
replies
1.6k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.6 years ago by
Basti
▴ 780 • written 3.6 years ago by
julie.hibbert
• 0
0
votes
2
replies
1.5k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 6 weeks ago by
Anni
• 0 • written 3.7 years ago by
hele7
▴ 20
0
votes
3
replies
4.5k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio
DEP
updated 3.7 years ago by
daniela.fuller
• 0 • written 3.9 years ago by
Tomaž
• 0
1
vote
7
replies
3.6k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData
Proteome
Database
DEP
3.7 years ago
tpm
• 0
1
vote
4
replies
1.9k
views
Failing to install DEP package. Some strange error.
R
Bioconductor
Install
DEP
3.8 years ago
tpm
• 0
0
votes
4
replies
1.4k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
3.8 years ago
rina
▴ 30
3
votes
7
replies
3.9k
views
Error when loading DEP in RStudio
dep
updated 3.9 years ago by
Desiree.
▴ 10 • written 4.2 years ago by
hele7
▴ 20
7
votes
2
replies
2.4k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 3.5 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 4.0 years ago by
Alexei Leliavski
▴ 60
0
votes
1
reply
959
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 4.1 years ago by
shepherl
4.1k • written 4.1 years ago by
tpm
• 0
3
votes
3
replies
1.3k
views
se does not inherit from class SummarizedExperiment
DEP
4.1 years ago
yueli7
▴ 20
0
votes
0
replies
803
views
Which package I can use?
MSnbase
DAPAR
DEP
4.1 years ago
yueli7
▴ 20
1
vote
1
reply
1.1k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.2 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 4.2 years ago by
justindean9208
▴ 10
1
vote
6
replies
3.6k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 4.4 years ago by
Laurent Gatto
1.6k • written 4.4 years ago by
jp
• 0
0
votes
1
reply
907
views
Error in generating heatmap
dep
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
nkvnambiar
• 0
1
vote
2
replies
2.0k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep
proteomics
limma
4.9 years ago
Rob
• 0
0
votes
0
replies
971
views
DEP package - Understanding the results table
dep
proteomics
logFC
5.2 years ago
rina
▴ 30
0
votes
0
replies
1.2k
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
5.2 years ago
dparrine
• 0
0
votes
0
replies
1.2k
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
5.3 years ago
tatabox
• 0
2
votes
3
replies
1.5k
views
DEP package: error in plot_heatmap
DEP
updated 5.3 years ago by
arne.smits
▴ 70 • written 5.3 years ago by
Rob
• 0
3
votes
3
replies
1.3k
views
Clarification of results tables in DEP
DEP
proteomics
updated 5.4 years ago by
arne.smits
▴ 70 • written 5.4 years ago by
António Miguel de Jesus Domingues
▴ 510
2
votes
8
replies
2.4k
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
5.4 years ago
Wuschel
▴ 10
1
vote
1
reply
989
views
DEP p.val adjustment
DEP
P.vals
adjustment
updated 5.7 years ago by
James W. MacDonald
67k • written 5.7 years ago by
826599
▴ 10
3
votes
2
replies
1.8k
views
DEP: Grouping Samples for missing value imputation
DEP
missing value imputation
proteomics
rforproteomics
7.0 years ago • updated 6.8 years ago
alex.gos90
▴ 10
2
votes
3
replies
2.5k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute
missing value imputation
DEP
massspectrometry
updated 7.0 years ago by
Laurent Gatto
1.6k • written 7.0 years ago by
serpalma.v
▴ 60
38 results • Page
1 of 1
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Replies
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
ATpoint
★ 4.6k
As said, literally identical on a continuous scale but different in categorical terms.
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
fjrsa
• 0
![enter image description here][1] [1]: /media/images/3d53e4b4-f561-41ee-a5d8-6c3c93e7
Answer: Advice needed: Using limma for differential pathway analysis with continuous dis
by
Gordon Smyth
52k
limma has always handled any combination of continuous or categorical variables from the very beginning. You simply add continuous variable…
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi @yangliao, thanks for the note. We use Feature Counts extensively for gene-level counting (exon features). Unfortunately though, and I…
Comment: Feature Counts - potential bug with outfile.jcounts
by
Yang Liao
▴ 450
When you use `featureCounts` to count junctions with the `-J` option, it doesn't check if the junction is exactly overlap with exons of gen…
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: Running multiple KNN queries in parallel
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