Showing : Proteomics • reset
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218
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limma/voom for protein intensity data
limma proteomics voom
updated 4 months ago by ▴ 970 • written 4 months ago by ▴ 60
0
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1
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153
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How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 4 months ago by 44k • written 4 months ago by • 0
0
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5
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241
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 5 months ago by 44k • written 5 months ago by • 0
0
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0
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130
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How to handle the imputation and normalisation?
Proteomics DEP limma
5 months ago barrypraveen • 0
0
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1
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198
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How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 6 months ago by • 0 • written 6 months ago by • 0
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299
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what is the difference between iBAQ or LFQ?
Proteomics DEP limma
6 months ago barrypraveen • 0
0
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4
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293
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How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
7 months ago barrypraveen • 0
4
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3
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681
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Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 10 months ago by 44k • written 10 months ago by ▴ 10
6
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6
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516
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 10 months ago by 44k • written 10 months ago by ▴ 10
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243
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Limma design multi-level experiment with 3 time points
R proteomics limma
10 months ago ellen2270 • 0
0
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4
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327
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DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
10 months ago rina ▴ 20
0
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305
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Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
11 months ago Robert Castelo ★ 2.8k
2
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1
reply
699
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Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 11 months ago by 58k • written 11 months ago by ★ 1.5k
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376
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Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
13 months ago Laura • 0
1
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2
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324
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calculate theoretical isotope distribution give the AA sequence
Metabolomics proteomics MassSpectrometry
13 months ago Oliver • 0
0
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3
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323
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Why I can not install rTANDEM?
MassSpectrometry Proteomics mzR
13 months ago Gilad • 0
1
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2
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327
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error in installation of 'org.Hs.eg.db'
proteomics GenomicSequence
updated 13 months ago by ▴ 60 • written 13 months ago by • 0
5
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6
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510
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possible package naming conflict
proteomics
13 months ago Tobias ▴ 30
1
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0
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308
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News: Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow proteomics Proteome
13 months ago info ▴ 10
0
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0
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191
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Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
14 months ago yueli7 ▴ 10
0
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1
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332
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R package to change protein *.msf file to any readable file
Proteome ProteomicsWorkflow proteomics
updated 14 months ago by ▴ 970 • written 14 months ago by ▴ 10
0
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0
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317
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Job: Data Scientist Proteomics (100%), Biozentrum, University of Basel, Switzerland
Switzerland JobPosting Basel Proteomics
14 months ago Robert Ivanek ▴ 710
0
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3
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462
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Find DEPs among TMT labeling proteom time course data by limma
limma proteomics TMTlabeling timecoursedata
updated 14 months ago by ▴ 270 • written 14 months ago by • 0
3
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0
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626
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Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
15 months ago Johannes Rainer ★ 1.9k
2
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0
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332
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Job: PostDoc position for the analysis of large scale metabolomics data
metabolomics proteomics Job
16 months ago Johannes Rainer ★ 1.9k
1
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6
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1.0k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 18 months ago by 1.5k • written 18 months ago by • 0
0
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0
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574
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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
software engineer RNASeq proteomics Job visualisation
19 months ago Laurent Gatto 1.5k
0
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0
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183
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How to generate custom MS database using CustomProDB?
r proteomics
21 months ago nattzy94 ▴ 10
2
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1
reply
317
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Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
22 months ago daniel.magnus.bader ▴ 40
2
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1
reply
281
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Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
23 months ago harelarik ▴ 50
1
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0
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310
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News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
23 months ago Laurent Gatto 1.5k
1
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2
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737
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Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
2.0 years ago Rob • 0
0
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0
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352
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Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
2.1 years ago lhuang7 ▴ 50
3
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0
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1.6k
views
Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
2.2 years ago • updated 2.1 years ago Gordon Smyth 44k
0
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0
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572
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News: May Institute Computation and statistics for mass spectrometry and proteomics
conference mass spectrometry proteomics News
2.1 years ago shepherl 2.9k
0
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0
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444
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News: course - Protemics with R and Bioconductor - 17-19 February 2020 in Berlin
Bioconductor R Proteomics News
2.2 years ago info ▴ 10
0
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0
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231
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proteoQC throwing error after running
ProteoQC Proteomics
2.2 years ago laural710 • 0
0
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2
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577
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Total Area Sum Intensity based Normalization for label-free quantitative proteomics
normalization proteomics label-free
2.2 years ago amolares • 0
0
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3
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581
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Writing a loop through multiple fasta files and named files (is it possible with MSGFplus?)
MSGF+ Proteomics r
updated 2.3 years ago by 25k • written 2.3 years ago by • 0
0
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0
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258
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DEP package - Understanding the results table
dep proteomics logFC
2.3 years ago rina ▴ 20
0
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0
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365
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DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
2.3 years ago dparrine • 0
2
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0
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1.7k
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Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
2.3 years ago Laurent Gatto 1.5k
0
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0
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291
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News: Protemics with R and Bioconductor course in Berlin
R Proteomics News
2.4 years ago info ▴ 10
0
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0
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372
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Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
2.4 years ago tatabox • 0
0
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8
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1.5k
views
Getting data into (and out of) the MSnSet object
proteomics MSnbase MSnSet readMSnSet msmsTests
updated 2.4 years ago by • 0 • written 4.0 years ago by ▴ 20
3
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3
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509
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Clarification of results tables in DEP
DEP proteomics
updated 2.5 years ago by ▴ 70 • written 2.5 years ago by ▴ 480
1
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3
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501
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Interpreting Fold Change Calculation in Limma to Non-Statisticians: Sanity Check
Limma proteomics limma
updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
2
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2
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403
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Where can I get functional bins for Arabidopsis thaliana genome (AGIs)
r proteomics RNA-Seq
updated 2.8 years ago by ▴ 180 • written 2.8 years ago by ▴ 10
0
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0
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349
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How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
2.8 years ago Wuschel ▴ 10
0
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2
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438
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Comparative proteome analysis of two different species
proteomics LC-MS/MS
updated 2.8 years ago by 1.5k • written 2.8 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Weird output of DESeq2 when using single sample from one group agains the other by Michael Love 35k
See the 2014 paper, the MLE LFC is found via IRLS: "We use the standard iteratively reweighted least-squares algorithm [12] for each gene’…
Comment: Weird output of DESeq2 when using single sample from one group agains the other by FantasticAI • 0
Thank you for the help. Sorry for keep asking silly questions: I wonder given 2 groups (A and B), and each group has 6 samples, how does th…
Answer: DESeq2 Responder vs Non-Responders nested design by Michael Love 35k
Unfortunately, I have to reserve my time on the support site for software related questions. For consultation about statistical design and …
Comment: How to use subjunc for differential splicing analysis? by Assa Yeroslaviz ★ 1.5k
I assume, that it would make more sense to quantify the reads based on the gene-level and not the exon-level, following by using the `diffS…
Comment: Reading large file (15GB) in R by nabiyogesh • 0
Thanks Sean, I am getting below error with fread, I am running this on HPC with 500GB. > library(data.table) data.table 1.14.2 u…
Votes
Where can I find EnsDb.Hsapiens.v105?
Two-way interaction, linear redundancy
Answer: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
Answer: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
Answer: Joint disperstion estimation for DEXSeq and DESeq2
Awards • All
Popular Question to svlachavas ▴ 780
Scholar to Michael Love 35k
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