Showing : DEP • reset
0
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301
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Warning while loading DEP package
DEP
updated 10 months ago by 4.1k • written 10 months ago by • 0
0
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3
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893
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 12 months ago by 52k • written 12 months ago by • 0
1
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2
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1.1k
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 20 months ago by ▴ 220 • written 21 months ago by ▴ 10
0
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0
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747
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
23 months ago aymanreffai • 0
0
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1
reply
661
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 23 months ago by ▴ 780 • written 24 months ago by • 0
0
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2
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826
views
Error message trying to open downloaded package
error DEP
2.1 years ago kcpaul168 • 0
0
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1
reply
848
views
Issue installing DEP package
DEP
updated 2.6 years ago by 4.1k • written 2.6 years ago by • 0
0
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7
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4.8k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.6 years ago by ★ 1.6k • written 3.0 years ago by ▴ 40
0
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0
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1.1k
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Introduction to DEP - data imputation
DEP impute
3.5 years ago catherine.li • 0
0
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0
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1.2k
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How to handle the imputation and normalisation?
Proteomics DEP limma
3.6 years ago barrypraveen • 0
0
votes
1
reply
1.1k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
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1
reply
1.5k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.6 years ago by • 0 • written 3.6 years ago by • 0
0
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0
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2.4k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.7 years ago by • 0
0
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0
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1.1k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.8 years ago hele7 ▴ 20
1
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3
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1.7k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.9 years ago by ▴ 780 • written 3.9 years ago by • 0
0
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2
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1.6k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 4 months ago by • 0 • written 3.9 years ago by ▴ 20
0
votes
3
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4.7k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 4.0 years ago by • 0 • written 4.2 years ago by • 0
1
vote
7
replies
3.8k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
4.0 years ago tpm • 0
1
vote
4
replies
2.0k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
4.0 years ago tpm • 0
0
votes
4
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1.4k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
4.0 years ago rina ▴ 30
3
votes
7
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4.0k
views
Error when loading DEP in RStudio
dep
updated 4.1 years ago by ▴ 10 • written 4.5 years ago by ▴ 20
7
votes
2
replies
2.5k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.7 years ago by ▴ 510 • written 4.3 years ago by ▴ 60
0
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1
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1.0k
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 4.3 years ago by 4.1k • written 4.3 years ago by • 0
3
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3
replies
1.4k
views
se does not inherit from class SummarizedExperiment
DEP
4.3 years ago yueli7 ▴ 20
0
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0
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852
views
Which package I can use?
MSnbase DAPAR DEP
4.3 years ago yueli7 ▴ 20
1
vote
1
reply
1.2k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.4 years ago by ▴ 510 • written 4.4 years ago by ▴ 10
1
vote
6
replies
3.8k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 4.6 years ago by 1.6k • written 4.6 years ago by • 0
0
votes
1
reply
983
views
Error in generating heatmap
dep
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
1
vote
2
replies
2.1k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
5.2 years ago Rob • 0
0
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0
replies
1.0k
views
DEP package - Understanding the results table
dep proteomics logFC
5.4 years ago rina ▴ 30
0
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0
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1.2k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.5 years ago • updated 5.4 years ago dparrine • 0
0
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0
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1.3k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.6 years ago tatabox • 0
2
votes
3
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1.6k
views
DEP package: error in plot_heatmap
DEP
updated 5.6 years ago by ▴ 70 • written 5.6 years ago by • 0
3
votes
3
replies
1.4k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.6 years ago by ▴ 70 • written 5.6 years ago by ▴ 510
2
votes
8
replies
2.6k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.6 years ago Wuschel ▴ 10
1
vote
1
reply
1.1k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 10
3
votes
2
replies
1.9k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
7.3 years ago • updated 7.1 years ago alex.gos90 ▴ 10
2
votes
3
replies
2.6k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 7.3 years ago by 1.6k • written 7.3 years ago by ▴ 60
38 results • Page 1 of 1
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Comment: sesameDataCache is not work properly on my system by Samreen • 0
Any luck with this? I have tried all of the above and it still doesn't work. This is my session info and I'm on a cluster computing environ…
Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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