Showing : proteomics • reset
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249
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Pathview visualisation not including positive log2 fold changes
pathview Proteomics
updated 8 weeks ago by 68k • written 8 weeks ago by • 0
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2
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496
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Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 3 months ago by ▴ 840
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0
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401
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Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
7 months ago Ragnhild • 0
3
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10
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1.4k
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 11 months ago by 68k • written 11 months ago by • 0
0
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3
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1.1k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
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0
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716
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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
13 months ago Peter Hickey ▴ 750
0
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1
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479
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analysis of overexpressed proteins in metaproteomes
Proteomics ProteoMM ProteomicsWorkflow Proteome
written 16 months ago by ▴ 10
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0
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506
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Normalising processed Proteomics data in R
Bioconductor Proteomics
17 months ago Joshua • 0
1
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4
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1.3k
views
How to find differentially expressed proteins from multiple conditions (>2) using proDA?
Proteomics proDA MultipleComparison
20 months ago • updated 19 months ago t.b.n.nguyen-9 • 0
1
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0
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728
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Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
20 months ago svlachavas ▴ 840
3
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4
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3.7k
views
Protein differential Expression analysis
differential expression proteomics
updated 20 months ago by ★ 4.8k • written 7.3 years ago by • 0
0
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1
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1.1k
views
R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics RforProteomics ProteomicsWorkflow Spectra MassSpectrometryData
updated 21 months ago by 1.6k • written 21 months ago by • 0
0
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5
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1.2k
views
R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics Proteomics ProteomicsWorkflow
updated 21 months ago by 1.6k • written 21 months ago by • 0
0
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2
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1.4k
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Proteomics data with NA values
Proteomics ProteoMM ProteomicsWorkflow
updated 21 months ago by • 0 • written 23 months ago by • 0
0
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2
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3.3k
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biomaRt to match UniProt protein IDs with protein names
Proteomics UniProtKeywords
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
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0
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1.1k
views
Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
2.1 years ago Laurent Gatto 1.6k
0
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0
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1.0k
views
Job: Open position in the CBIO lab: spatial proteomics and PTMs
pRoloc proteomics Spatial Proteomics MassSpectrometry
2.1 years ago Laurent Gatto 1.6k
0
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0
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794
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
2.2 years ago info ▴ 10
0
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1
reply
1.1k
views
Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
updated 2.2 years ago by 1.6k • written 4.4 years ago by ▴ 20
1
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3
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1.8k
views
Adding ellipse in PCAtools biplot
Biplot FactoMineR proteomics PCAtools ellipse
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by • 0
1
vote
0
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927
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
2.3 years ago Arend ▴ 10
3
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3
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2.2k
views
Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
0
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0
replies
791
views
A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
2.4 years ago Abdullah • 0
0
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0
replies
1.0k
views
Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
cancer bioinformatics proteomics genomics phd
2.4 years ago DKFZ International PhD Program ▴ 10
1
vote
3
replies
1.3k
views
Proteomics-time series with repeated measures
Proteomics limma repeatedmeasures TimeSeriesExperiment
2.5 years ago proteome_AO • 0
0
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5
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1.5k
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Inquiry about suitable package for proteomics study design
Proteomics design
updated 2.5 years ago by • 0 • written 2.5 years ago by • 0
0
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0
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808
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Outliers
Proteomics Proteome
updated 2.6 years ago by ★ 4.8k • written 2.6 years ago by • 0
0
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0
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741
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Finding DEGs between two different datasets using limma
Proteomics limma proteomi
2.6 years ago mfaleevs • 0
0
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3
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1.3k
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 2.7 years ago by 52k • written 2.7 years ago by • 0
1
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0
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1.1k
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Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics Proteomics Cancer Statistics Bioinformatics
2.7 years ago Andy Lynch ▴ 120
0
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0
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1.1k
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
2.7 years ago qiz218591 • 0
2
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5
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2.7k
views
proteomics analysis
Proteomics analysis
updated 2.8 years ago by ▴ 90 • written 2.8 years ago by • 0
1
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2
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1.4k
views
Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2 ProteomicsWorkflow proteomics
updated 2.9 years ago by 52k • written 3.0 years ago by ▴ 10
2
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1
reply
1.4k
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Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
1
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0
replies
1.0k
views
Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
phd cancer genomics proteomics bioinformatics
3.0 years ago DKFZ International PhD Program ▴ 10
0
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0
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1.0k
views
ProteoMM analysis with two replicates
shotgunproteomics Proteome proteomics Proteomics ProteoMM
3.1 years ago ary.lech ▴ 10
0
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2
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2.4k
views
Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 3.2 years ago by 52k • written 3.2 years ago by • 0
0
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0
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1.0k
views
Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
3.2 years ago Robert Castelo ★ 3.4k
0
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1
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2.8k
views
limma/voom for protein intensity data
limma proteomics voom
updated 3.6 years ago by ★ 4.8k • written 3.6 years ago by ▴ 70
0
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1
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979
views
How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 3.6 years ago by 52k • written 3.6 years ago by • 0
0
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5
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1.5k
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 3.7 years ago by 52k • written 3.7 years ago by • 0
0
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0
replies
1.3k
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How to handle the imputation and normalisation?
Proteomics DEP limma
3.7 years ago barrypraveen • 0
0
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1
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1.6k
views
How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.8 years ago by • 0 • written 3.8 years ago by • 0
0
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0
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2.5k
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what is the difference between iBAQ or LFQ?
Proteomics DEP limma
written 3.8 years ago by • 0
0
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4
replies
1.7k
views
How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
updated 2.0 years ago by 52k • written 3.8 years ago by • 0
5
votes
6
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5.6k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 15 months ago by • 0 • written 4.1 years ago by ▴ 10
6
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6
replies
2.2k
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 4.1 years ago by 52k • written 4.1 years ago by ▴ 10
0
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0
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1.2k
views
Limma design multi-level experiment with 3 time points
R proteomics limma
4.1 years ago ellen2270 • 0
0
votes
4
replies
1.5k
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
4.1 years ago rina ▴ 30
0
votes
0
replies
1.3k
views
Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
4.2 years ago Robert Castelo ★ 3.4k
50 results • Page 1 of 1
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Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - I appreciate the mathematical explanation and link to Dr. Phipson's thesis!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - this is very clear!
Answer: How do I set up my DESeq analysis when I know a few vehicle control samples prov by Michael Love 43k
I think it will capture it automatically. E.g. if you use the method that focuses on genes lowly or not affected by the treatment, then the…
Votes
Comment: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
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