Showing : DEP • reset
1
vote
2
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274
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Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 10 weeks ago by ▴ 180 • written 3 months ago by ▴ 10
0
votes
0
replies
224
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
5 months ago aymanreffai • 0
0
votes
1
reply
225
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 6 months ago by ▴ 720 • written 6 months ago by • 0
0
votes
2
replies
327
views
Error message trying to open downloaded package
error DEP
7 months ago kcpaul168 • 0
0
votes
1
reply
375
views
Issue installing DEP package
DEP
updated 13 months ago by 3.5k • written 13 months ago by • 0
0
votes
7
replies
2.7k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 13 months ago by ★ 1.6k • written 19 months ago by ▴ 40
0
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0
replies
603
views
Introduction to DEP - data imputation
DEP impute
2.1 years ago catherine.li • 0
0
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0
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617
views
How to handle the imputation and normalisation?
Proteomics DEP limma
2.1 years ago barrypraveen • 0
0
votes
1
reply
621
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 2.2 years ago by 63k • written 2.2 years ago by • 0
0
votes
1
reply
818
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 2.2 years ago by • 0 • written 2.2 years ago by • 0
0
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0
replies
1.3k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.2 years ago by • 0
0
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0
replies
578
views
How to obtain log2 intensity per sample in DEP?
DEP
2.3 years ago hele7 ▴ 20
1
vote
3
replies
1.1k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 2.4 years ago by ▴ 720 • written 2.4 years ago by • 0
0
votes
1
reply
801
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 6 months ago by • 0 • written 2.5 years ago by ▴ 20
0
votes
3
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3.7k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 2.5 years ago by • 0 • written 2.7 years ago by • 0
1
vote
7
replies
2.6k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
2.6 years ago • updated 2.5 years ago tpm • 0
1
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4
replies
1.2k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
2.6 years ago tpm • 0
0
votes
4
replies
847
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
2.6 years ago rina ▴ 20
3
votes
7
replies
3.1k
views
Error when loading DEP in RStudio
dep
updated 2.7 years ago by ▴ 10 • written 3.0 years ago by ▴ 20
7
votes
2
replies
1.5k
views
False discovery rates in DEP
p-value FDR DEP
updated 2.3 years ago by ▴ 490 • written 2.8 years ago by ▴ 60
0
votes
1
reply
609
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 2.9 years ago by 3.5k • written 2.9 years ago by • 0
3
votes
3
replies
717
views
se does not inherit from class SummarizedExperiment
DEP
2.9 years ago yueli7 ▴ 20
0
votes
0
replies
470
views
Which package I can use?
MSnbase DAPAR DEP
2.9 years ago yueli7 ▴ 20
1
vote
1
reply
669
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 3.0 years ago by ▴ 490 • written 3.0 years ago by ▴ 10
1
vote
6
replies
2.8k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.2 years ago by 1.6k • written 3.2 years ago by • 0
0
votes
1
reply
554
views
Error in generating heatmap
dep
updated 3.4 years ago by 3.8k • written 3.4 years ago by • 0
1
vote
2
replies
1.5k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
3.7 years ago Rob • 0
0
votes
0
replies
613
views
DEP package - Understanding the results table
dep proteomics logFC
4.0 years ago rina ▴ 20
0
votes
0
replies
756
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
4.0 years ago dparrine • 0
0
votes
0
replies
769
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.1 years ago tatabox • 0
2
votes
3
replies
1.0k
views
DEP package: error in plot_heatmap
DEP
updated 4.1 years ago by ▴ 70 • written 4.2 years ago by • 0
3
votes
3
replies
891
views
Clarification of results tables in DEP
DEP proteomics
updated 4.2 years ago by ▴ 70 • written 4.2 years ago by ▴ 490
2
votes
8
replies
1.5k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.2 years ago Wuschel ▴ 10
1
vote
1
reply
617
views
DEP p.val adjustment
DEP P.vals adjustment
updated 4.5 years ago by 63k • written 4.5 years ago by ▴ 10
3
votes
2
replies
1.3k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
5.8 years ago • updated 5.6 years ago alex.gos90 ▴ 10
2
votes
3
replies
1.8k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 5.8 years ago by 1.6k • written 5.8 years ago by ▴ 60
36 results • Page 1 of 1
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Answer: Problems with FLOWAI by SHASHI • 0
Additionally, if you're looking to clean FCS data files, you can utilize an R script. I've prepared a comprehensive YouTube tutorial to aid…
Answer: Is SeqSQC compatible with hg38? by James W. MacDonald 63k
I'll answer your question with a question. Is there any reason to believe that things like IBD or PCA or Sex checks would be dependent on t…
Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of by Gregory • 0
Thanks for the prompt response, Gordon. I'm looking for count at the gene level - the gene id is the meta feature, so one row per gene in …
Comment: DiffBind handling of replicates and consensus by Rory Stark ★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles) by Rory Stark ★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Votes
Answer: How do I merge a list of GRanges?
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
Comment: DiffBind: dba.plotProfile(profiles)
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
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