Bioconductor ProteomicsWorkflow

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limma ProteomicsWorkflow

updated 7 months ago by Gordon Smyth 50k • written 2.5 years ago by David Lyon ▴ 340

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Proteomics ProteomicsWorkflow UniProt.ws

updated 3.2 years ago by James W. MacDonald 65k • written 3.2 years ago by Dario Strbenac ★ 1.5k

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ProteomicsWorkflow proteomics Proteome

3.4 years ago info ▴ 10

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Proteome ProteomicsWorkflow proteomics

updated 3.4 years ago by swbarnes2 ★ 1.3k • written 3.4 years ago by yueli7 ▴ 20

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916

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msqrob2 ProteomicsWorkflow proteomics

updated 22 months ago by Gordon Smyth 50k • written 23 months ago by Jane ▴ 10

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913

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limma Proteomics ProteomicsWorkflow

updated 20 months ago by Gordon Smyth 50k • written 20 months ago by samantha.v.goncalves • 0

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814

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ProteomicsWorkflow proteomics proteinProfiles

updated 13 months ago by Laurent Gatto 1.6k • written 3.4 years ago by yueli7 ▴ 20

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Proteomics ProteoMM ProteomicsWorkflow

updated 8 months ago by mmvar • 0 • written 10 months ago by nkvnambiar • 0

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730

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proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics

updated 2.6 years ago by Gordon Smyth 50k • written 2.6 years ago by ALOK • 0

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704

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RforProteomics Proteomics ProteomicsWorkflow

updated 8 months ago by Laurent Gatto 1.6k • written 8 months ago by mmvar • 0

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574

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Proteomics RforProteomics ProteomicsWorkflow Spectra MassSpectrometryData

updated 8 months ago by Laurent Gatto 1.6k • written 8 months ago by mmvar • 0

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184

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Proteomics ProteoMM ProteomicsWorkflow Proteome

written 4 months ago by ary.lech ▴ 10

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Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k

Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.

Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100

See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…

Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850

This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…

Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k

Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…

Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k

I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…

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Comment: DEXSeq DEXSeqDataSet count matrix duplication

Comment: Error in champ.load(): The following specified files do not exist

Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos

Using GRanges and IRanges to simply get all chromosome data

A: Using GRanges and IRanges to simply get all chromosome data

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