Showing : DEP • reset
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
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
985
views
se does not inherit from class SummarizedExperiment
DEP
3.5 years ago yueli7 ▴ 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
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
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
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
2
votes
8
replies
2.0k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.8 years ago Wuschel ▴ 10
1
vote
6
replies
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
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
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
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
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
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
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
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
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
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
0
votes
1
reply
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
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
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
3
replies
316
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
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
0
replies
949
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.7 years ago • updated 4.6 years ago dparrine • 0
0
votes
0
replies
809
views
DEP package - Understanding the results table
dep proteomics logFC
4.6 years ago rina ▴ 30
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
0
votes
0
replies
661
views
Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
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
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
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
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
595
views
Issue installing DEP package
DEP
updated 21 months ago by 3.9k • written 21 months ago by • 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
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
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!!
Votes
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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