Showing : DEP • reset
0
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276
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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
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801
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 months ago by 52k • written 10 months ago by • 0
1
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2
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991
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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705
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
633
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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777
views
Error message trying to open downloaded package
error DEP
23 months ago kcpaul168 • 0
0
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1
reply
791
views
Issue installing DEP package
DEP
updated 2.5 years ago by 4.1k • written 2.5 years ago by • 0
0
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7
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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
3.4 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 3.5 years ago by • 0
0
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0
replies
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 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
0
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2
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1.5k
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Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 12 weeks 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 • updated 3.8 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
replies
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
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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 4.1 years ago by ▴ 60
0
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1
reply
989
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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820
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
932
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
votes
0
replies
997
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
5.3 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 5.4 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 6.9 years ago alex.gos90 ▴ 10
2
votes
3
replies
2.5k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute missing value imputation DEP massspectrometry
updated 7.1 years ago by 1.6k • written 7.1 years ago by ▴ 60
38 results • Page 1 of 1
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Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
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How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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