Showing : DEP • reset
1
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6
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3.2k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.8 years ago by 1.6k • written 3.8 years ago by • 0
3
votes
2
replies
1.5k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
6.5 years ago • updated 6.3 years ago alex.gos90 ▴ 10
0
votes
1
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1.2k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 2.8 years ago by • 0 • written 2.8 years ago by • 0
3
votes
7
replies
3.6k
views
Error when loading DEP in RStudio
dep
updated 3.3 years ago by ▴ 10 • written 3.7 years ago by ▴ 20
3
votes
3
replies
1.1k
views
Clarification of results tables in DEP
DEP proteomics
updated 4.8 years ago by ▴ 70 • written 4.8 years ago by ▴ 510
0
votes
3
replies
316
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
2
votes
3
replies
2.2k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 6.5 years ago by 1.6k • written 6.5 years ago by ▴ 60
1
vote
1
reply
802
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 10
2
votes
3
replies
1.3k
views
DEP package: error in plot_heatmap
DEP
updated 4.8 years ago by ▴ 70 • written 4.8 years ago by • 0
0
votes
1
reply
734
views
Error in generating heatmap
dep
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
1
vote
1
reply
861
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.6 years ago by ▴ 510 • written 3.6 years ago by ▴ 10
3
votes
3
replies
985
views
se does not inherit from class SummarizedExperiment
DEP
3.5 years ago yueli7 ▴ 20
0
votes
3
replies
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
1
vote
7
replies
3.2k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
3.2 years ago tpm • 0
0
votes
7
replies
3.5k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 21 months ago by ★ 1.6k • written 2.2 years ago by ▴ 40
0
votes
1
reply
856
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
1
vote
3
replies
1.4k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
0
votes
2
replies
563
views
Error message trying to open downloaded package
error DEP
15 months ago kcpaul168 • 0
0
votes
1
reply
444
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
0
votes
0
replies
920
views
How to handle the imputation and normalisation?
Proteomics DEP limma
2.8 years ago barrypraveen • 0
0
votes
4
replies
1.1k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.2 years ago rina ▴ 30
1
vote
4
replies
1.6k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
3.2 years ago tpm • 0
1
vote
2
replies
686
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 10 months ago by ▴ 210 • written 11 months ago by ▴ 10
0
votes
0
replies
824
views
How to obtain log2 intensity per sample in DEP?
DEP
2.9 years ago hele7 ▴ 20
0
votes
0
replies
132
views
Warning while loading DEP package
DEP
updated 28 days ago by 3.9k • written 28 days ago by • 0
0
votes
1
reply
596
views
Issue installing DEP package
DEP
updated 21 months ago by 3.9k • written 21 months ago by • 0
0
votes
0
replies
495
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
13 months ago aymanreffai • 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 3.1 years ago by ▴ 20
0
votes
0
replies
810
views
Introduction to DEP - data imputation
DEP impute
2.7 years ago catherine.li • 0
0
votes
0
replies
809
views
DEP package - Understanding the results table
dep proteomics logFC
4.6 years ago rina ▴ 30
1
vote
2
replies
1.8k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.3 years ago Rob • 0
0
votes
0
replies
1.8k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.8 years ago by • 0
0
votes
0
replies
949
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.7 years ago • updated 4.6 years ago dparrine • 0
2
votes
8
replies
2.0k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.8 years ago Wuschel ▴ 10
0
votes
0
replies
661
views
Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
0
votes
0
replies
1.0k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
0
votes
1
reply
802
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 3.5 years ago by 3.9k • written 3.5 years ago by • 0
7
votes
2
replies
2.0k
views
False discovery rates in DEP
p-value FDR DEP
updated 2.9 years ago by ▴ 510 • written 3.5 years ago by ▴ 60
38 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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