Showing : Proteomics • reset
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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 11 minutes ago by 46k • written 6 days ago by • 0
1
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Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics Proteomics Cancer Statistics Bioinformatics
22 days ago Andy Lynch ▴ 120
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82
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About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
22 days ago qiz218591 • 0
2
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5
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274
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proteomics analysis
Proteomics analysis
updated 5 weeks ago by ▴ 70 • written 5 weeks ago by • 0
1
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2
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200
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Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2 ProteomicsWorkflow proteomics
updated 10 weeks ago by 46k • written 3 months ago by • 0
2
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1
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190
views
Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 3 months ago by 60k • written 3 months ago by • 0
1
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0
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151
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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
3 months ago DKFZ International PhD Program ▴ 10
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0
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133
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ProteoMM analysis with two replicates
shotgunproteomics Proteome proteomics Proteomics ProteoMM
5 months ago ary.lech ▴ 10
0
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2
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461
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Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 6 months ago by 46k • written 6 months ago by • 0
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221
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Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
6 months ago Robert Castelo ★ 2.9k
0
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1
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449
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limma/voom for protein intensity data
limma proteomics voom
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 60
0
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1
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255
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How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 11 months ago by 46k • written 11 months ago by • 0
0
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5
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395
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 11 months ago by 46k • written 11 months ago by • 0
0
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0
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242
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How to handle the imputation and normalisation?
Proteomics DEP limma
12 months ago barrypraveen • 0
0
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1
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340
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How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 13 months ago by • 0 • written 13 months ago by • 0
0
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0
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540
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what is the difference between iBAQ or LFQ?
Proteomics DEP limma
13 months ago barrypraveen • 0
0
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4
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409
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How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
13 months ago barrypraveen • 0
4
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3
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1.2k
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Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 17 months ago by 46k • written 17 months ago by ▴ 10
6
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6
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754
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 17 months ago by 46k • written 17 months ago by ▴ 10
0
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412
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Limma design multi-level experiment with 3 time points
R proteomics limma
17 months ago ellen2270 • 0
0
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4
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438
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DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
17 months ago rina ▴ 20
0
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423
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Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
18 months ago Robert Castelo ★ 2.9k
2
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1
reply
1.5k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 18 months ago by 60k • written 18 months ago by ★ 1.5k
0
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491
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Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
20 months ago Laura • 0
1
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2
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454
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calculate theoretical isotope distribution give the AA sequence
Metabolomics proteomics MassSpectrometry
20 months ago Oliver • 0
0
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3
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447
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Why I can not install rTANDEM?
MassSpectrometry Proteomics mzR
20 months ago Gilad • 0
1
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2
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442
views
error in installation of 'org.Hs.eg.db'
proteomics GenomicSequence
updated 20 months ago by ▴ 70 • written 20 months ago by • 0
5
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6
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740
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possible package naming conflict
proteomics
20 months ago Tobias ▴ 30
1
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503
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News: Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow proteomics Proteome
20 months ago info ▴ 10
0
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259
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Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
20 months ago yueli7 ▴ 20
0
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1
reply
424
views
R package to change protein *.msf file to any readable file
Proteome ProteomicsWorkflow proteomics
updated 21 months ago by ★ 1.1k • written 21 months ago by ▴ 20
0
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0
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427
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Job: Data Scientist Proteomics (100%), Biozentrum, University of Basel, Switzerland
Switzerland JobPosting Basel Proteomics
21 months ago Robert Ivanek ▴ 730
0
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3
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634
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Find DEPs among TMT labeling proteom time course data by limma
limma proteomics TMTlabeling timecoursedata
updated 21 months ago by ▴ 270 • written 21 months ago by • 0
3
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0
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1.0k
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Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
22 months ago Johannes Rainer ★ 2.0k
2
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0
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437
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Job: PostDoc position for the analysis of large scale metabolomics data
metabolomics proteomics Job
23 months ago Johannes Rainer ★ 2.0k
1
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6
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1.5k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 2.1 years ago by 1.6k • written 2.1 years ago by • 0
0
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0
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687
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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
software engineer RNASeq proteomics Job visualisation
2.2 years ago Laurent Gatto 1.6k
0
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0
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253
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How to generate custom MS database using CustomProDB?
r proteomics
2.3 years ago nattzy94 ▴ 20
2
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1
reply
428
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Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
2.4 years ago daniel.magnus.bader ▴ 40
2
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1
reply
448
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Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
2.5 years ago harelarik ▴ 50
1
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493
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News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
2.5 years ago Laurent Gatto 1.6k
1
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2
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1.0k
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Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
2.6 years ago Rob • 0
0
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0
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466
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Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
2.6 years ago lhuang7 ▴ 50
3
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1.7k
views
Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
2.8 years ago • updated 2.6 years ago Gordon Smyth 46k
0
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690
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News: May Institute Computation and statistics for mass spectrometry and proteomics
conference mass spectrometry proteomics News
2.7 years ago shepherl 3.2k
0
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523
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News: course - Protemics with R and Bioconductor - 17-19 February 2020 in Berlin
Bioconductor R Proteomics News
2.7 years ago info ▴ 10
0
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0
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293
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proteoQC throwing error after running
ProteoQC Proteomics
2.8 years ago laural710 • 0
0
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2
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760
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Total Area Sum Intensity based Normalization for label-free quantitative proteomics
normalization proteomics label-free
2.8 years ago amolares • 0
0
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3
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821
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Writing a loop through multiple fasta files and named files (is it possible with MSGFplus?)
MSGF+ Proteomics r
updated 2.8 years ago by 25k • written 2.8 years ago by • 0
0
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0
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336
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DEP package - Understanding the results table
dep proteomics logFC
2.9 years ago rina ▴ 20
50 results • Page 1 of 1
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Answer: Design and contrast matrices for analyzing the effect of two factors of interest by Gordon Smyth 46k
> In a typical regression, I would just add them to the model when estimating my coefficients of interest Why not do the same with limma? …
Comment: TPM normalization starting with read counts by Gordon Smyth 46k
> So you think my method in TPM normalization that I introduced above is not good? You have computed RPKMs, not TPMs. None of my software …
Comment: error in package GenVisR while installing by 堃 • 0
Package ‘FField’ was removed from the CRAN repository.[enter link description here][1] I installed FField by using remotes::install_github…
Comment: DESeq 2 failes to load by Ruggero • 0
This solved the error, in case someone else is having compilation errors from installing RSQllite: install.packages('RSQLite', repos='http…
Comment: pathview says my nonmodel species is unknown: "species invalid" by Guido Hooiveld ★ 3.3k
A while ago a faced the same for another non-model organism. I was able to get it working using a 'hack'. This hack is nothing more than m…
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Answer: How to remove dendrogram from pheatmaps?
A: conceptual question about FDR, FDR adjusted p-value and q-value
A: conceptual question about FDR, FDR adjusted p-value and q-value
A: How to select summit size for histone ChiP-Seq in Diffbind
Answer: Unable to download supplementary files from GSE146963 using GEOquery
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