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ProteomicsWorkflow
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217
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analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 5 months ago by
ary.lech
▴ 10
6
votes
5
replies
6.3k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 8 months ago by
Gordon Smyth
50k • written 2.5 years ago by
David Lyon
▴ 340
0
votes
1
reply
634
views
R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics
RforProteomics
ProteomicsWorkflow
Spectra
MassSpectrometryData
updated 9 months ago by
Laurent Gatto
1.6k • written 9 months ago by
mmvar
• 0
0
votes
5
replies
765
views
R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics
Proteomics
ProteomicsWorkflow
updated 9 months ago by
Laurent Gatto
1.6k • written 9 months ago by
mmvar
• 0
0
votes
2
replies
832
views
Proteomics data with NA values
Proteomics
ProteoMM
ProteomicsWorkflow
updated 9 months ago by
mmvar
• 0 • written 11 months ago by
nkvnambiar
• 0
0
votes
1
reply
847
views
Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow
proteomics
proteinProfiles
updated 14 months ago by
Laurent Gatto
1.6k • written 3.5 years ago by
yueli7
▴ 20
0
votes
3
replies
943
views
Design and contrast matrices for analyzing the effect of two factors of interest on protein expression, controlling for factors and covariates not of…
limma
Proteomics
ProteomicsWorkflow
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
samantha.v.goncalves
• 0
1
vote
2
replies
946
views
Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2
ProteomicsWorkflow
proteomics
updated 23 months ago by
Gordon Smyth
50k • written 2.0 years ago by
Jane
▴ 10
0
votes
1
reply
761
views
How to pull-down gene/protein names from the database search, using R ?
proteinProfiles
ProteomicsWorkflow
ProteomicsAnnotationHubData
Proteomics
updated 2.7 years ago by
Gordon Smyth
50k • written 2.7 years ago by
ALOK
• 0
2
votes
1
reply
3.1k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics
ProteomicsWorkflow
UniProt.ws
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
Dario Strbenac
★ 1.5k
1
vote
0
replies
1.5k
views
News:
Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow
proteomics
Proteome
3.5 years ago
info
▴ 10
0
votes
1
reply
1.1k
views
R package to change protein *.msf file to any readable file
Proteome
ProteomicsWorkflow
proteomics
updated 3.5 years ago by
swbarnes2
★ 1.4k • written 3.5 years ago by
yueli7
▴ 20
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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
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
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