Showing : Proteomics • reset
1
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How to find differentially expressed proteins from multiple conditions (>2) using proDA?
Proteomics proDA MultipleComparison
27 days ago • updated 25 days ago t.b.n.nguyen-9 • 0
0
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0
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124
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Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
29 days ago svlachavas ▴ 810
3
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4
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2.4k
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Protein differential Expression analysis
differential expression proteomics
updated 5 weeks ago by ★ 3.4k • written 5.7 years ago by • 0
0
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1
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158
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R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics RforProteomics ProteomicsWorkflow Spectra MassSpectrometryData
updated 8 weeks ago by 1.6k • written 8 weeks ago by • 0
0
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5
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283
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R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics Proteomics ProteomicsWorkflow
updated 8 weeks ago by 1.6k • written 8 weeks ago by • 0
0
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2
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329
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Proteomics data with NA values
Proteomics ProteoMM ProteomicsWorkflow
updated 8 weeks ago by • 0 • written 3 months ago by • 0
0
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2
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460
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biomaRt to match UniProt protein IDs with protein names
Proteomics UniProtKeywords
updated 6 months ago by 63k • written 6 months ago by • 0
0
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0
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289
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
6 months ago Laurent Gatto 1.6k
0
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0
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291
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Job: Open position in the CBIO lab: spatial proteomics and PTMs
pRoloc proteomics Spatial Proteomics MassSpectrometry
6 months ago Laurent Gatto 1.6k
0
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0
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244
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News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
7 months ago info ▴ 10
0
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1
reply
565
views
Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
updated 7 months ago by 1.6k • written 2.8 years ago by ▴ 20
1
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3
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642
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Adding ellipse in PCAtools biplot
Biplot FactoMineR proteomics PCAtools ellipse
updated 8 months ago by 3.8k • written 8 months ago by • 0
1
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0
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300
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Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
8 months ago Arend ▴ 10
3
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3
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711
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Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 8 months ago by 48k • written 8 months ago by • 0
0
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0
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278
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A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
10 months ago Abdullah • 0
0
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0
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402
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Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
cancer bioinformatics proteomics genomics phd
10 months ago DKFZ International PhD Program ▴ 10
1
vote
3
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606
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Proteomics-time series with repeated measures
Proteomics limma repeatedmeasures TimeSeriesExperiment
11 months ago • updated 10 months ago proteome_AO • 0
0
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5
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634
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Inquiry about suitable package for proteomics study design
Proteomics design
updated 11 months ago by • 0 • written 11 months ago by • 0
0
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0
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325
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Outliers
Proteomics Proteome
updated 12 months ago by ★ 3.4k • written 12 months ago by • 0
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0
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257
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Finding DEGs between two different datasets using limma
Proteomics limma proteomi
12 months ago mfaleevs • 0
0
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3
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641
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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 13 months ago by 48k • written 13 months ago by • 0
1
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0
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425
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Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics Proteomics Cancer Statistics Bioinformatics
14 months ago Andy Lynch ▴ 120
0
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0
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439
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About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
14 months ago qiz218591 • 0
2
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5
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1.1k
views
proteomics analysis
Proteomics analysis
updated 14 months ago by ▴ 90 • written 14 months ago by • 0
1
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2
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622
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Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2 ProteomicsWorkflow proteomics
updated 15 months ago by 48k • written 16 months ago by • 0
2
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1
reply
644
views
Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 16 months ago by 63k • written 16 months ago by • 0
1
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0
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499
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Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
phd cancer genomics proteomics bioinformatics
17 months ago DKFZ International PhD Program ▴ 10
0
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0
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517
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ProteoMM analysis with two replicates
shotgunproteomics Proteome proteomics Proteomics ProteoMM
18 months ago ary.lech ▴ 10
0
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2
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1.3k
views
Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 19 months ago by 48k • written 19 months ago by • 0
0
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0
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542
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Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
20 months ago Robert Castelo ★ 3.0k
0
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1
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1.2k
views
limma/voom for protein intensity data
limma proteomics voom
updated 2.0 years ago by ★ 3.4k • written 2.0 years ago by ▴ 70
0
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1
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558
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How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 2.1 years ago by 48k • written 2.1 years ago by • 0
0
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5
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826
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 2.1 years ago by 48k • written 2.1 years ago by • 0
0
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0
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609
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How to handle the imputation and normalisation?
Proteomics DEP limma
2.1 years ago barrypraveen • 0
0
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1
reply
815
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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
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0
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1.3k
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what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 2.2 years ago by • 0
0
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4
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881
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How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
updated 5 months ago by 48k • written 2.3 years ago by • 0
4
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3
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2.7k
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Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 2.5 years ago by 48k • written 2.5 years ago by ▴ 10
6
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6
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1.3k
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 2.5 years ago by 48k • written 2.5 years ago by ▴ 10
0
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0
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753
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Limma design multi-level experiment with 3 time points
R proteomics limma
2.5 years ago ellen2270 • 0
0
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4
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837
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DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
2.6 years ago rina ▴ 20
0
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0
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745
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Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
2.6 years ago Robert Castelo ★ 3.0k
2
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1
reply
2.5k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 2.6 years ago by 63k • written 2.6 years ago by ★ 1.5k
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0
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833
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Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
2.8 years ago Laura • 0
1
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2
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875
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calculate theoretical isotope distribution give the AA sequence
Metabolomics proteomics MassSpectrometry
2.8 years ago Oliver • 0
0
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3
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839
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Why I can not install rTANDEM?
MassSpectrometry Proteomics mzR
2.8 years ago Gilad • 0
1
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2
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838
views
error in installation of 'org.Hs.eg.db'
proteomics GenomicSequence
updated 2.8 years ago by ▴ 90 • written 2.8 years ago by • 0
5
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6
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1.2k
views
possible package naming conflict
proteomics
2.8 years ago Tobias ▴ 40
1
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0
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1.2k
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News: Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow proteomics Proteome
2.8 years ago info ▴ 10
0
votes
1
reply
863
views
R package to change protein *.msf file to any readable file
Proteome ProteomicsWorkflow proteomics
updated 2.8 years ago by ★ 1.3k • written 2.8 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
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Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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