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DEP
•
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0
votes
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replies
261
views
Warning while loading DEP package
DEP
updated 7 months ago by
shepherl
4.1k • written 7 months ago by
Namrata
• 0
0
votes
3
replies
726
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 9 months ago by
Gordon Smyth
52k • written 9 months ago by
Laura
• 0
1
vote
2
replies
957
views
Error running run_app('LFQ')
LFQ
DEPpackage
run_app('LFQ')
ShinyApps
DEP
updated 17 months ago by
Ram
▴ 220 • written 18 months ago by
d.kozhevnikova
▴ 10
0
votes
0
replies
682
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
20 months ago
aymanreffai
• 0
0
votes
1
reply
614
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 21 months ago by
Basti
▴ 780 • written 21 months ago by
fuqichen1
• 0
0
votes
2
replies
753
views
Error message trying to open downloaded package
error
DEP
22 months ago
kcpaul168
• 0
0
votes
1
reply
769
views
Issue installing DEP package
DEP
updated 2.4 years ago by
shepherl
4.1k • written 2.4 years ago by
dheeraj.raya
• 0
0
votes
7
replies
4.4k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 2.3 years ago by
Malcolm Cook
★ 1.6k • written 2.8 years ago by
Tobias
▴ 40
0
votes
0
replies
995
views
Introduction to DEP - data imputation
DEP
impute
3.3 years ago
catherine.li
• 0
0
votes
0
replies
1.1k
views
How to handle the imputation and normalisation?
Proteomics
DEP
limma
3.3 years ago
barrypraveen
• 0
0
votes
1
reply
1.0k
views
Gene ontology of differentially expressed genes in R
topGO
limma
DEP
updated 3.4 years ago by
James W. MacDonald
67k • written 3.4 years ago by
pedarf
• 0
0
votes
1
reply
1.4k
views
How to remove batch effect on DEP protemics package?
Proteomics
DEP
MassSpectrometryData
updated 3.4 years ago by
bigomics.team
• 0 • written 3.4 years ago by
barrypraveen
• 0
0
votes
0
replies
2.3k
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
written 3.4 years ago by
barrypraveen
• 0
0
votes
0
replies
1.1k
views
How to obtain log2 intensity per sample in DEP?
DEP
3.5 years ago
hele7
▴ 20
1
vote
3
replies
1.6k
views
Error installing DEP in Rstudio on MacBook
DEP
updated 3.6 years ago by
Basti
▴ 780 • written 3.6 years ago by
julie.hibbert
• 0
0
votes
2
replies
1.5k
views
Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
updated 7 weeks ago by
Anni
• 0 • written 3.7 years ago by
hele7
▴ 20
1
vote
7
replies
3.6k
views
How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData
Proteome
Database
DEP
3.8 years ago • updated 3.7 years ago
tpm
• 0
1
vote
4
replies
1.9k
views
Failing to install DEP package. Some strange error.
R
Bioconductor
Install
DEP
3.8 years ago
tpm
• 0
0
votes
4
replies
1.4k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics
DEP
3.8 years ago
rina
▴ 30
0
votes
3
replies
4.5k
views
GMM/DEP Package lib/libgomp.1.dylib: mach-o, but wrong architecture
ProblemloadingDEP/GMMpackageinRStudio
DEP
updated 3.7 years ago by
daniela.fuller
• 0 • written 3.9 years ago by
Tomaž
• 0
7
votes
2
replies
2.4k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 3.5 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 4.0 years ago by
Alexei Leliavski
▴ 60
0
votes
1
reply
960
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 4.1 years ago by
shepherl
4.1k • written 4.1 years ago by
tpm
• 0
3
votes
3
replies
1.3k
views
se does not inherit from class SummarizedExperiment
DEP
4.1 years ago
yueli7
▴ 20
0
votes
0
replies
804
views
Which package I can use?
MSnbase
DAPAR
DEP
4.1 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 4.2 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 4.2 years ago by
justindean9208
▴ 10
3
votes
7
replies
3.9k
views
Error when loading DEP in RStudio
dep
updated 3.9 years ago by
Desiree.
▴ 10 • written 4.2 years ago by
hele7
▴ 20
1
vote
6
replies
3.6k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 4.4 years ago by
Laurent Gatto
1.6k • written 4.4 years ago by
jp
• 0
0
votes
1
reply
909
views
Error in generating heatmap
dep
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
nkvnambiar
• 0
1
vote
2
replies
2.0k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep
proteomics
limma
4.9 years ago
Rob
• 0
0
votes
0
replies
974
views
DEP package - Understanding the results table
dep
proteomics
logFC
5.2 years ago
rina
▴ 30
0
votes
0
replies
1.2k
views
DEP: TMT analysis from MaxQuant output
DEP
TMT
proteomics
5.2 years ago
dparrine
• 0
0
votes
0
replies
1.2k
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
5.3 years ago
tatabox
• 0
2
votes
3
replies
1.5k
views
DEP package: error in plot_heatmap
DEP
updated 5.3 years ago by
arne.smits
▴ 70 • written 5.4 years ago by
Rob
• 0
2
votes
8
replies
2.4k
views
Error: se does not inherit from class SummarizedExperiment
DEP
SummarizedExperiment
5.4 years ago
Wuschel
▴ 10
3
votes
3
replies
1.3k
views
Clarification of results tables in DEP
DEP
proteomics
updated 5.4 years ago by
arne.smits
▴ 70 • written 5.4 years ago by
António Miguel de Jesus Domingues
▴ 510
1
vote
1
reply
992
views
DEP p.val adjustment
DEP
P.vals
adjustment
updated 5.7 years ago by
James W. MacDonald
67k • written 5.7 years ago by
826599
▴ 10
2
votes
3
replies
2.5k
views
Imputation method selection (mass spectrometry) bimodal distribution
impute
missing value imputation
DEP
massspectrometry
updated 7.0 years ago by
Laurent Gatto
1.6k • written 7.0 years ago by
serpalma.v
▴ 60
3
votes
2
replies
1.8k
views
DEP: Grouping Samples for missing value imputation
DEP
missing value imputation
proteomics
rforproteomics
7.0 years ago • updated 6.8 years ago
alex.gos90
▴ 10
38 results • Page
1 of 1
Recent ...
Replies
Comment: Help using rtracklayer for gene ID extraction
by
James W. MacDonald
67k
Telling me you can't do something without showing what you tried is not helpful. When posting here, try to put yourself in the shoes of peo…
Comment: miRTarRnaseq library
by
María Calvo
• 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Answer: Need new version : tx2gene.gencode.v47.csv
by
Guido Hooiveld
★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Comment: Help using rtracklayer for gene ID extraction
by
Aichatou
• 0
Hello, Please disregard the previous post. it's working now, i think. I am able to create the txdb object but I can't see all the other inf…
Comment: p value is 0, padj is 0
by
Wirayatida
• 0
Than you so much. My counts are 47,37 and 72 for mock. The treatment is 8153, 6723 and 8024.
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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