Showing : proteomics • reset
0
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284
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Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
3 months ago Ragnhild • 0
3
votes
10
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1.1k
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 7 months ago by 67k • written 7 months ago by • 0
0
votes
3
replies
814
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 7 months ago by ★ 4.6k • written 7 months ago by • 0
0
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0
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594
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Job: Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics JobPosting SingleCell Spatial SpatialExperiment
9 months ago Peter Hickey ▴ 740
0
votes
1
reply
407
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analysis of overexpressed proteins in metaproteomes
Proteomics ProteoMM ProteomicsWorkflow Proteome
written 12 months ago by ▴ 10
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0
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423
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Normalising processed Proteomics data in R
Bioconductor Proteomics
13 months ago Joshua • 0
1
vote
4
replies
1.1k
views
How to find differentially expressed proteins from multiple conditions (>2) using proDA?
Proteomics proDA MultipleComparison
16 months ago • updated 15 months ago t.b.n.nguyen-9 • 0
1
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0
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646
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
16 months ago svlachavas ▴ 840
3
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4
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3.5k
views
Protein differential Expression analysis
differential expression proteomics
updated 16 months ago by ★ 4.6k • written 7.0 years ago by • 0
0
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1
reply
963
views
R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics RforProteomics ProteomicsWorkflow Spectra MassSpectrometryData
updated 17 months ago by 1.6k • written 17 months ago by • 0
0
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5
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1.1k
views
R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics Proteomics ProteomicsWorkflow
updated 17 months ago by 1.6k • written 17 months ago by • 0
0
votes
2
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1.2k
views
Proteomics data with NA values
Proteomics ProteoMM ProteomicsWorkflow
updated 17 months ago by • 0 • written 19 months ago by • 0
0
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2
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2.5k
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biomaRt to match UniProt protein IDs with protein names
Proteomics UniProtKeywords
updated 21 months ago by 67k • written 21 months ago by • 0
0
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0
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876
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
21 months ago Laurent Gatto 1.6k
0
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0
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903
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Job: Open position in the CBIO lab: spatial proteomics and PTMs
pRoloc proteomics Spatial Proteomics MassSpectrometry
22 months ago Laurent Gatto 1.6k
0
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0
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719
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News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
22 months ago info ▴ 10
0
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1
reply
1.0k
views
Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
updated 22 months ago by 1.6k • written 4.1 years ago by ▴ 20
1
vote
3
replies
1.5k
views
Adding ellipse in PCAtools biplot
Biplot FactoMineR proteomics PCAtools ellipse
updated 23 months ago by ★ 4.0k • written 23 months ago by • 0
1
vote
0
replies
808
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
23 months ago Arend ▴ 10
3
votes
3
replies
1.9k
views
Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 23 months ago by 52k • written 24 months ago by • 0
0
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0
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728
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A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
2.1 years ago Abdullah • 0
0
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0
replies
919
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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
2.1 years ago DKFZ International PhD Program ▴ 10
1
vote
3
replies
1.2k
views
Proteomics-time series with repeated measures
Proteomics limma repeatedmeasures TimeSeriesExperiment
2.2 years ago • updated 2.1 years ago proteome_AO • 0
0
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5
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1.3k
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 2.2 years ago by • 0 • written 2.2 years ago by • 0
0
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0
replies
738
views
Outliers
Proteomics Proteome
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by • 0
0
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0
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643
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Finding DEGs between two different datasets using limma
Proteomics limma proteomi
2.3 years ago mfaleevs • 0
0
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3
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1.2k
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 2.3 years ago by 52k • written 2.4 years ago by • 0
1
vote
0
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1.0k
views
Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics Proteomics Cancer Statistics Bioinformatics
2.4 years ago Andy Lynch ▴ 120
0
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0
replies
980
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About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
2.4 years ago qiz218591 • 0
2
votes
5
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2.4k
views
proteomics analysis
Proteomics analysis
updated 2.5 years ago by ▴ 90 • written 2.5 years ago by • 0
1
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2
replies
1.2k
views
Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2 ProteomicsWorkflow proteomics
updated 2.5 years ago by 52k • written 2.6 years ago by ▴ 10
2
votes
1
reply
1.3k
views
Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 2.6 years ago by 67k • written 2.6 years ago by • 0
1
vote
0
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915
views
Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
phd cancer genomics proteomics bioinformatics
2.7 years ago DKFZ International PhD Program ▴ 10
0
votes
0
replies
925
views
ProteoMM analysis with two replicates
shotgunproteomics Proteome proteomics Proteomics ProteoMM
2.8 years ago ary.lech ▴ 10
0
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2
replies
2.2k
views
Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 2.9 years ago by 52k • written 2.9 years ago by • 0
0
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0
replies
947
views
Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
2.9 years ago Robert Castelo ★ 3.4k
0
votes
1
reply
2.5k
views
limma/voom for protein intensity data
limma proteomics voom
updated 3.3 years ago by ★ 4.6k • written 3.3 years ago by ▴ 70
0
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1
reply
912
views
How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 3.3 years ago by 52k • written 3.3 years ago by • 0
0
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5
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1.4k
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 3.3 years ago by 52k • written 3.3 years ago by • 0
0
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0
replies
1.1k
views
How to handle the imputation and normalisation?
Proteomics DEP limma
3.4 years ago barrypraveen • 0
0
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1
reply
1.4k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.4 years ago by • 0 • written 3.4 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 3.4 years ago by • 0
0
votes
4
replies
1.5k
views
How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
updated 20 months ago by 52k • written 3.5 years ago by • 0
5
votes
6
replies
5.0k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 11 months ago by • 0 • written 3.8 years ago by ▴ 10
6
votes
6
replies
2.0k
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 3.8 years ago by 52k • written 3.8 years ago by ▴ 10
0
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0
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1.1k
views
Limma design multi-level experiment with 3 time points
R proteomics limma
3.8 years ago ellen2270 • 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
0
replies
1.1k
views
Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
3.8 years ago Robert Castelo ★ 3.4k
2
votes
1
reply
3.7k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 3.9 years ago by 67k • written 3.9 years ago by ★ 1.5k
0
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0
replies
1.3k
views
Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
4.0 years ago Laura • 0
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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
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Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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