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Showing top results for tag: proteomics • reset
1
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131
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Finding Differential Phosphosites in TMT Phosphoproteomics Data
DEqMS Mass Phosphoproteomics Proteomics Spec
updated 1 day ago by 85k • written 1 day ago by • 0
1
vote
2
replies
169
views
Dealing with outliers for differential expression in proteomics
proteomics PCA DEA outliers limma
updated 2 days ago by 85k • written 2 days ago by • 0
0
votes
2
replies
189
views
Reconciling old crystallography papers with modern sequencing data
PDB proteomics
updated 19 hours ago by ★ 2.1k • written 2 days ago by ▴ 310
2
votes
2
replies
170
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statistical testing for MS/MS proteomics bulk samples
DEG proteomics
updated 3 days ago by 85k • written 4 days ago by ▴ 60
2
votes
1
reply
254
views
Best protein imputation method when comparing knock-outs?
imputation proteomics mass-spectrometry MS LFQ
updated 8 days ago by ▴ 100 • written 8 days ago by ▴ 30
7
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5
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3.1k
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Limma: is it necessary to log-transform the data?
proteomics limma
updated 12 days ago by ★ 7.5k • written 19 months ago by • 0
0
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4
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525
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Looking for proteins play role in cardiovascular diseases (disease ontology)
proteomics protein uniprot disease-ontology
5 weeks ago by Bendegúz • 0
0
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1
reply
529
views
Tandem Mass Tag (TMT) proteomics data analysis
tmt tandem-mass-tag proteomics
updated 6 weeks ago by 44k • written 2.7 years ago by • 0
0
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0
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262
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Comparative proteomics using online mass spec data
Mass-spectrometry proteomics
updated 6 weeks ago by 44k • written 6 weeks ago by ▴ 20
0
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0
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268
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LFQ values from MS counts
MS LFQ proteomics mass-spectrometry
updated 6 weeks ago by 44k • written 7 weeks ago by ▴ 30
4
votes
2
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344
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Weird looking volcano plot
Proteomics Volcano-plot Plasma
updated 7 weeks ago by ▴ 30 • written 7 weeks ago by • 0
1
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2
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392
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topGO R package - how to account for fold expression and p value
R proteomics topGO enrichment
11 weeks ago by Sven • 0
0
votes
2
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357
views
Batch correction for protein data
proteomics DESeq2 batch-correction
9 weeks ago by 4732b159 • 0
3
votes
2
replies
408
views
is that statistical correct to use DEseq2 for proteomics data
proteomics DEseq2
updated 3 months ago by 85k • written 3 months ago by ▴ 60
0
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2
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237
views
MAXLFQ peptide data analysis
chemoproteomics proteomics MAXLFQ
3 months ago by SHN ▴ 40
0
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6
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640
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DESeq2 for DE analysis of proteins
proteomics DESeq2
updated 3 months ago by ★ 6.9k • written 3 months ago by • 0
3
votes
2
replies
378
views
Statistical analysis of quantified proteomic data: ctrl vs. mut
statistics proteomics
updated 4 months ago by 85k • written 4 months ago by • 0
0
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0
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221
views
What is the reason for the requirement of at least 2 experiments for LFQ in MaxQuant?
MaxQuant Spectrometry Mass Proteomics LFQ
4 months ago by Riq ▴ 50
0
votes
1
reply
341
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Help with proteomics downstream analysis
mass-spectrometry proteomics
updated 5 months ago by 44k • written 5 months ago by • 0
1
vote
0
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244
views
Simulation of label-free bottom-up proteomics expression dataset
label-free bottom-up lc-ms proteomics
6 months ago by KABILAN ▴ 100
0
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0
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292
views
Lncipedia GTF file error
Proteomics
updated 6 months ago by 44k • written 6 months ago by ▴ 40
3
votes
7
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813
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Integration of transcriptomics and proteomics: difficult matching names
rna-seq tmt nomenclature proteomics
6 months ago by ntsopoul ▴ 60
1
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3
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4.2k
views
MSF Data Analysis
MSF Proteomics Thermo Proteome Discoverer
updated 7 months ago by • 0 • written 4.9 years ago by ▴ 130
0
votes
3
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485
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Resources regarding Proteomics (In-Silico)
molecular-simulation docking protein proteomics
updated 7 months ago by 44k • written 7 months ago by • 0
3
votes
1
reply
574
views
Job: AN INTEGRATED IN SILICO AND IN VITRO STUDY ON THE DEVELOPMENT OF A COMPUTATIONAL METHOD FOR THE PREDICTION OF O-GLCNAC MODIFIED PROTEINS
proteomics
updated 8 months ago by 44k • written 8 months ago by • 0
1
vote
3
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882
views
Job: 1 Bioinformatician position in San Sebastian (Spain)
postdoc phd proteomics scRNAseq transcriptomics
8 months ago by ev97 ▴ 40
1
vote
2
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444
views
How to visualize unique and overlapping genes in upSet R plot
R Proteomics UpsetR
8 months ago by S'bonelo Glen • 0
0
votes
0
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310
views
News: Online course: R/Bioconductor for Mass Spectrometry and Proteomics
R Proteomics Bioconductor Mass-Spectrometry
updated 8 months ago by 44k • written 8 months ago by ★ 2.6k
0
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0
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249
views
Proteomics : imputation of missing values in all replicates
proteomics
8 months ago by lagartija ▴ 160
0
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0
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337
views
Struggling to use the compare cluster function in Cluster Profiler
R proteomics
updated 8 months ago by 44k • written 8 months ago by • 0
1
vote
1
reply
337
views
fold change value
proteomics gene-expression
updated 8 months ago by 44k • written 8 months ago by • 0
2
votes
5
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950
views
Physical Protein size
proteomics databases
updated 8 months ago by 55k • written 9 months ago by ▴ 170
1
vote
4
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635
views
Molecular docking with Autodock
Docking proteomics
updated 6 months ago by 44k • written 9 months ago by ▴ 10
1
vote
1
reply
506
views
Optimal network construction strategy to investigate interactions between proteins and metabolites in more than one disease
networks metabolomics proteomics cytoscape
updated 9 months ago by ▴ 280 • written 9 months ago by • 0
1
vote
3
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890
views
how to download BF ,CC and MF
proteomics
updated 9 months ago by ▴ 420 • written 9 months ago by ▴ 20
0
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0
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213
views
Correlating Chip-Seq and proteimics results
chip-seq correlations proteomics
9 months ago by Assa Yeroslaviz ★ 1.9k
1
vote
2
replies
450
views
How to get differntial Protein expression from protein abundance?
Proteomics protein DEPs Abundance
updated 24 days ago by • 0 • written 9 months ago by • 0
0
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1
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395
views
Proteomic data search and analysis
Proteomics
updated 10 months ago by ★ 2.5k • written 10 months ago by ▴ 10
0
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2
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566
views
enrichment site for pathogen protein interaction in host plant genome
genomics proteomics
10 months ago by shwetamgr1 ▴ 10
5
votes
2
replies
753
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics proteomics multiomics
updated 10 months ago by 4.5k • written 11 months ago by ▴ 810
0
votes
0
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329
views
Is there any s/w that can be used to map metabolite results to it's pathway/s?
R metabolomics proteomics Python
10 months ago by WUSCHEL ▴ 810
0
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2
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553
views
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
translation Variant proteomics FASTA VCF
11 months ago by chscho • 0
0
votes
0
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328
views
Any one familiar with IP-MS data analysis?
IP-MS proteomics differential expression analysis
12 months ago by shuaizh117 ▴ 10
0
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1
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348
views
How to reduce the redundance in proteomic dataset
proteomics
updated 12 months ago by 146k • written 12 months ago by • 0
0
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0
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301
views
processing and downstream analysis of mzxml files in R
Proteomics mzXML
12 months ago by 1769mkc ★ 1.2k
2
votes
4
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1.1k
views
Database for cell lines, genes and proteins associated with them
proteomics cell-line
updated 14 months ago by ▴ 120 • written 15 months ago by ▴ 40
2
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5
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1.2k
views
Uniprot Database for download
proteomics Uniprot
updated 13 months ago by ★ 2.4k • written 14 months ago by ▴ 40
0
votes
4
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766
views
WGS sequencing data based proteomics analysis
workflow UniProt proteomics WGS RNA-Seq
updated 15 months ago by ★ 1.2k • written 15 months ago by ★ 1.9k
0
votes
0
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344
views
Confusion regarding the normalization of TMT experiment with multiple plexes: Healthy + Tumor Together
proteomics normalization TMT
16 months ago by kts.desilva • 0
0
votes
1
reply
792
views
Publish Olink data in a proteomics database
proteomics Olink
16 months ago by Lluís R. ★ 1.2k
50 results • Page 1 of 1
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Comment: Finding Differential Phosphosites in TMT Phosphoproteomics Data
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Comment: Magnesium ion in a post-docking adjustment by dthorbur ★ 2.5k
[`AlphaFold3`](https://alphafoldserver.com/) (assuming you're not at conflict with their terms of use) can handle both ligands and ions. An…
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation by Chen • 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
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The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
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I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
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What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
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The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
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Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
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The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
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What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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