Showing : Proteomics • reset
25
votes
9
replies
6.0k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 8.7 years ago by 48k • written 8.7 years ago by ▴ 40
8
votes
2
replies
2.5k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts proteomics limma edger deseq
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 60
8
votes
0
replies
3.3k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
8.2 years ago Martin Morgan 25k
6
votes
6
replies
1.3k
views
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
5
votes
3
replies
1.6k
views
Strong upwards correlation between log fold change and average log expression in MD plot of Limma
limma proteomics
updated 5.9 years ago by 48k • written 5.9 years ago by • 0
5
votes
6
replies
1.2k
views
possible package naming conflict
proteomics
2.8 years ago Tobias ▴ 40
4
votes
9
replies
1.8k
views
Limma is doing the right way to calculate the fold change?
limma proteomics
updated 6.3 years ago by 1.6k • written 6.3 years ago by ▴ 30
4
votes
5
replies
1.6k
views
How to convert a xlsx data file to MSnSet format?
msnbase msmstests proteomics lc-ms/ms msnID
updated 4.6 years ago by 1.6k • written 4.6 years ago by ▴ 10
4
votes
3
replies
2.7k
views
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
3
votes
0
replies
1.9k
views
Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
3.9 years ago • updated 3.7 years ago Gordon Smyth 48k
3
votes
3
replies
701
views
Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 8 months ago by 48k • written 8 months ago by • 0
3
votes
4
replies
1.5k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 5.9 years ago by ▴ 150 • written 5.9 years ago by ▴ 10
3
votes
4
replies
1.1k
views
Writing a loop to clean up protein names
Proteomics Transcriptomics Loops batch-processing R
updated 5.0 years ago by ▴ 80 • written 5.0 years ago by • 0
3
votes
2
replies
1.2k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
5.8 years ago • updated 5.6 years ago alex.gos90 ▴ 10
3
votes
3
replies
885
views
Clarification of results tables in DEP
DEP proteomics
updated 4.2 years ago by ▴ 70 • written 4.2 years ago by ▴ 490
3
votes
4
replies
2.4k
views
Protein differential Expression analysis
differential expression proteomics
updated 4 weeks ago by ★ 3.4k • written 5.7 years ago by • 0
3
votes
0
replies
1.7k
views
Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
2.9 years ago Johannes Rainer ★ 2.0k
2
votes
0
replies
2.1k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
4.0 years ago Laurent Gatto 1.6k
2
votes
2
replies
694
views
Where can I get functional bins for Arabidopsis thaliana genome (AGIs)
r proteomics RNA-Seq
updated 4.5 years ago by ▴ 180 • written 4.5 years ago by ▴ 10
2
votes
7
replies
1.3k
views
I get nothing in my up and down regulated genes
limma proteomics label free
7.1 years ago Nemo ▴ 80
2
votes
0
replies
1.0k
views
mapping protein PTM data
proteomics
5.9 years ago petyuk ▴ 70
2
votes
12
replies
1.4k
views
msmsTests, NA values in test.results output
Proteomics msmstests FDR
updated 4.9 years ago by 1.6k • written 4.9 years ago by • 0
2
votes
5
replies
1.1k
views
proteomics analysis
Proteomics analysis
updated 14 months ago by ▴ 90 • written 14 months ago by • 0
2
votes
0
replies
972
views
News: LAST CHANCE: May Institute 2018 - Computation and statistics for mass spectrometry and proteomics at Northeastern University in Boston
news proteomics course training msstats News
5.7 years ago mnchoi67 ▴ 40
2
votes
4
replies
1.2k
views
how to find up regulated proteins from a label free
deseq2 proteomics label free
updated 7.1 years ago by 1.6k • written 7.1 years ago by ▴ 80
2
votes
1
reply
636
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
2
votes
1
reply
1.5k
views
News: Announcing a short course in computational and statistical proteomics
proteomics massspectrometry R News
8.7 years ago vitek.olga ▴ 20
2
votes
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
2
votes
0
replies
728
views
Job: PostDoc position for the analysis of large scale metabolomics data
metabolomics proteomics Job
3.0 years ago Johannes Rainer ★ 2.0k
2
votes
1
reply
925
views
Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
3.6 years ago harelarik ▴ 60
2
votes
5
replies
1.4k
views
NA coefficients values for samples with all zeros
limmagui proteomics
7.8 years ago vedran.franke • 0
2
votes
1
reply
730
views
Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
3.5 years ago daniel.magnus.bader ▴ 40
2
votes
3
replies
1.1k
views
rTANDEM package -- An R encapsulation of the X!Tandem algorithm
Proteomics rTANDEM Proteomics rTANDEM
updated 10.8 years ago by 13k • written 10.8 years ago by ▴ 40
2
votes
1
reply
1.9k
views
DESeq package
Proteomics DESeq Proteomics DESeq
updated 10.9 years ago by ▴ 550 • written 10.9 years ago by ▴ 20
1
vote
3
replies
813
views
Interpreting Fold Change Calculation in Limma to Non-Statisticians: Sanity Check
Limma proteomics limma
updated 4.3 years ago by • 0 • written 4.3 years ago by • 0
1
vote
2
replies
685
views
Errors installing "shinyTANDEM" package
software error proteomics
updated 4.5 years ago by 1.6k • written 4.5 years ago by • 0
1
vote
2
replies
1.7k
views
Errors installing mzR package
proteomics error
updated 4.5 years ago by 1.6k • written 4.5 years ago by • 0
1
vote
1
reply
879
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
4.9 years ago Sebastian Hesse ▴ 70
1
vote
1
reply
1.2k
views
News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 4.6 years ago by 1.6k
1
vote
2
replies
2.4k
views
Limma: technical and biological replicates in proteomics data
limma proteomics replicates
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
1
vote
6
replies
2.8k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.2 years ago by 1.6k • written 3.2 years ago by • 0
1
vote
3
replies
1.1k
views
Running GO analysis via Prostar
prostar proteomics rforproteomics annotationforge
updated 5.3 years ago by ▴ 10 • written 5.3 years ago by ▴ 20
1
vote
0
replies
1.4k
views
Job: Full time and permanent research logistician in Bioinformatics
transcriptomics proteomics job bioinformatician Job
4.6 years ago • updated 4.5 years ago Laurent Gatto 1.6k
1
vote
2
replies
1.5k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
3.7 years ago Rob • 0
1
vote
1
reply
1.7k
views
Job: junior level position in proteomics/data science
proteomics machine learning git docker Job
updated 5.7 years ago by • 0 • written 6.0 years ago by ▴ 70
1
vote
0
replies
1.7k
views
News: May Institute 2018 - Computation and statistics for mass spectrometry and proteomics at Northeastern University in Boston
bioconductor training course msstats proteomics News
5.7 years ago mnchoi67 ▴ 40
1
vote
1
reply
1.1k
views
Job: Post-doctoral mass spectrometry and proteomics bioinformatician (updated)
bioinformatics proteomics mass spectrometry job Job
6.3 years ago • updated 6.2 years ago Laurent Gatto 1.6k
1
vote
2
replies
1.3k
views
Deseq2 with replicate mean and variance information
deseq2 deseq differential analysis proteomics
5.5 years ago blehtine • 0
1
vote
1
reply
5.2k
views
Mfuzz: fill.NA - Warning messages: argument is not numeric or logical: returning NA
mfuzz clustering bioinformatics proteomics timecourse
updated 7.6 years ago by 1.6k • written 7.6 years ago by • 0
1
vote
8
replies
1.8k
views
DESEQ2 and continuous data
proteomics deseq2
7.7 years ago • updated 7.6 years ago carandres74 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DMRcate design by Jitendra ▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Votes
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
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