Showing : DEP • reset
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48
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Warning while loading DEP package
DEP
updated 1 day ago by 3.8k • written 1 day ago by • 0
0
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3
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264
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
1
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2
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639
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 9 months ago by ▴ 190 • written 10 months ago by ▴ 10
0
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0
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471
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
12 months ago aymanreffai • 0
0
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1
reply
419
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How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 13 months ago by ▴ 770 • written 13 months ago by • 0
0
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2
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532
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Error message trying to open downloaded package
error DEP
14 months ago kcpaul168 • 0
0
votes
1
reply
573
views
Issue installing DEP package
DEP
updated 20 months ago by 3.8k • written 20 months ago by • 0
0
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7
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3.4k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 20 months ago by ★ 1.6k • written 2.1 years ago by ▴ 40
0
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0
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775
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Introduction to DEP - data imputation
DEP impute
2.6 years ago catherine.li • 0
0
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0
replies
888
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How to handle the imputation and normalisation?
Proteomics DEP limma
2.7 years ago barrypraveen • 0
0
votes
1
reply
832
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
0
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1
reply
1.1k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 2.7 years ago by • 0 • written 2.8 years ago by • 0
0
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0
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1.7k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.8 years ago by • 0
0
votes
0
replies
778
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago hele7 ▴ 20
1
vote
3
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1.4k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.0 years ago by ▴ 770 • written 3.0 years ago by • 0
0
votes
1
reply
1.1k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 13 months ago by • 0 • written 3.0 years ago by ▴ 20
1
vote
7
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3.1k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
3.1 years ago tpm • 0
1
vote
4
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1.5k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
3.1 years ago tpm • 0
0
votes
4
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1.1k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.1 years ago rina ▴ 30
0
votes
3
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4.1k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 3.1 years ago by • 0 • written 3.3 years ago by • 0
7
votes
2
replies
1.9k
views
False discovery rates in DEP
p-value FDR DEP
updated 2.8 years ago by ▴ 490 • written 3.4 years ago by ▴ 60
0
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1
reply
778
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 3.4 years ago by 3.8k • written 3.4 years ago by • 0
3
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3
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955
views
se does not inherit from class SummarizedExperiment
DEP
3.4 years ago yueli7 ▴ 20
0
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0
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640
views
Which package I can use?
MSnbase DAPAR DEP
3.4 years ago yueli7 ▴ 20
1
vote
1
reply
842
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.5 years ago by ▴ 490 • written 3.5 years ago by ▴ 10
3
votes
7
replies
3.5k
views
Error when loading DEP in RStudio
dep
updated 3.2 years ago by ▴ 10 • written 3.6 years ago by ▴ 20
1
vote
6
replies
3.2k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.7 years ago by 1.6k • written 3.7 years ago by • 0
0
votes
1
reply
719
views
Error in generating heatmap
dep
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 0
1
vote
2
replies
1.7k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.3 years ago Rob • 0
0
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0
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792
views
DEP package - Understanding the results table
dep proteomics logFC
4.5 years ago rina ▴ 30
0
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0
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929
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.6 years ago dparrine • 0
0
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0
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984
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
2
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3
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1.3k
views
DEP package: error in plot_heatmap
DEP
updated 4.7 years ago by ▴ 70 • written 4.7 years ago by • 0
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.7 years ago Wuschel ▴ 10
3
votes
3
replies
1.1k
views
Clarification of results tables in DEP
DEP proteomics
updated 4.7 years ago by ▴ 70 • written 4.8 years ago by ▴ 490
1
vote
1
reply
783
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
2
votes
3
replies
2.1k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 6.4 years ago by 1.6k • written 6.4 years ago by ▴ 60
3
votes
2
replies
1.5k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
6.4 years ago • updated 6.2 years ago alex.gos90 ▴ 10
38 results • Page 1 of 1
Recent ...
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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