Showing : DEP • reset
0
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279
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Warning while loading DEP package
DEP
updated 9 months ago by 4.1k • written 9 months ago by • 0
0
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3
replies
817
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 months ago by 52k • written 11 months ago by • 0
1
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2
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1000
views
Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 18 months ago by ▴ 220 • written 19 months ago by ▴ 10
0
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0
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714
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
21 months ago aymanreffai • 0
0
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1
reply
638
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
0
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2
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786
views
Error message trying to open downloaded package
error DEP
24 months ago • updated 23 months ago kcpaul168 • 0
0
votes
1
reply
799
views
Issue installing DEP package
DEP
updated 2.5 years ago by 4.1k • written 2.5 years ago by • 0
0
votes
7
replies
4.5k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.5 years ago by ★ 1.6k • written 2.9 years ago by ▴ 40
0
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0
replies
1.0k
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Introduction to DEP - data imputation
DEP impute
3.4 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
3.5 years ago barrypraveen • 0
0
votes
1
reply
1.1k
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 3.5 years ago by 67k • written 3.5 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 3.5 years ago by • 0 • written 3.5 years ago by • 0
0
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0
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2.3k
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.6 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
3.6 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 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
0
votes
2
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1.5k
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Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 3 months ago by • 0 • written 3.8 years ago by ▴ 20
0
votes
3
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4.6k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio DEP
updated 3.8 years ago by • 0 • written 4.0 years ago by • 0
1
vote
7
replies
3.7k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
3.9 years ago tpm • 0
1
vote
4
replies
1.9k
views
Failing to install DEP package. Some strange error.
R Bioconductor Install DEP
3.9 years ago tpm • 0
0
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4
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1.4k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
3.9 years ago rina ▴ 30
3
votes
7
replies
4.0k
views
Error when loading DEP in RStudio
dep
updated 4.0 years ago by ▴ 10 • written 4.4 years ago by ▴ 20
7
votes
2
replies
2.4k
views
False discovery rates in DEP
p-value FDR DEP
updated 3.6 years ago by ▴ 510 • written 4.2 years ago by ▴ 60
0
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1
reply
994
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 4.2 years ago by 4.1k • written 4.2 years ago by • 0
3
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3
replies
1.3k
views
se does not inherit from class SummarizedExperiment
DEP
4.2 years ago yueli7 ▴ 20
0
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0
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824
views
Which package I can use?
MSnbase DAPAR DEP
4.2 years ago yueli7 ▴ 20
1
vote
1
reply
1.1k
views
Using DEP package with continuous variable for condition, rather than categorical in SummarizedExperiment object
dep
updated 4.3 years ago by ▴ 510 • written 4.3 years ago by ▴ 10
1
vote
6
replies
3.7k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 4.5 years ago by 1.6k • written 4.5 years ago by • 0
0
votes
1
reply
940
views
Error in generating heatmap
dep
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
1
vote
2
replies
2.0k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
5.0 years ago Rob • 0
0
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0
replies
1.0k
views
DEP package - Understanding the results table
dep proteomics logFC
5.3 years ago rina ▴ 30
0
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0
replies
1.2k
views
DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
5.4 years ago • updated 5.3 years ago dparrine • 0
0
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0
replies
1.2k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.4 years ago tatabox • 0
2
votes
3
replies
1.5k
views
DEP package: error in plot_heatmap
DEP
updated 5.5 years ago by ▴ 70 • written 5.5 years ago by • 0
3
votes
3
replies
1.4k
views
Clarification of results tables in DEP
DEP proteomics
updated 5.5 years ago by ▴ 70 • written 5.5 years ago by ▴ 510
2
votes
8
replies
2.5k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.5 years ago Wuschel ▴ 10
1
vote
1
reply
1.0k
views
DEP p.val adjustment
DEP P.vals adjustment
updated 5.8 years ago by 67k • written 5.8 years ago by ▴ 10
3
votes
2
replies
1.8k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
7.2 years ago • updated 7.0 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 7.2 years ago by 1.6k • written 7.2 years ago by ▴ 60
38 results • Page 1 of 1
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Replies
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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