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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
author recetox
date Wed, 22 Jan 2025 07:44:00 +0000
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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1 <macros>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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3 <token name="@GENERAL_HELP@">
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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4 Scp Help section
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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5 ===================
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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7 Overview
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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8 --------
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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9 The `scp` tool facilitates the processing of the mass spectrometry-based single cell proteomics (SCP) data. It builds on the `scp` R package developed in the laboratory of prof. Laurent Gatto and provides functions for the peptide-to-spectrum match (PSM), peptide or protein-level filtering, normalization, transformation and imputation of missing values.
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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11 The source code can be found in the following Github repository or on BioConductor:
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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12 .. _GitHub: https://github.com/UCLouvain-CBIO/scp/
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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13 .. _issues: https://github.com/UCLouvain-CBIO/scp/issues
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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14 .. _Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/scp.html
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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16 Workflow
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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17 --------
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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19 The scp workflow currently supports the processing of MaxQuant results and requires two input files:
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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21 - evidence.txt file (output from MaxQuant)
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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22 - sampleAnnotation file (provided by user). The SampleAnnotation file is a metadata file, describing annotation of individual samples (such as quantification column names, batches, sample types, etc.). Please note, that the run identifier column MUST be present in both evidence and sampleAnnotation files.
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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24 The workflow starts at the level of PSM. Firstly, the data are filtered extensively to keep only the most reliable identifications: reverse sequences and potential contaminants are removed, as well as PSMs below certain parental ion fraction threshold or not passing a q-value threshold. Also batches with very few features are excluded.
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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26 Subsequently, PSMs are aggregated to peptide level. On the peptide level, another filtering is applied based on median relative intensity or median CV. Peptide-level intensities are then normalized and log2 transformed.
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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28 Such intensities are then further aggregated to the protein level, where they undergo another normalization and imputation of missing values.
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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30 Because of the unavoidable batch effects present in the single-cell data, scp offers two methods for the batch correction: ComBat and removeBatchEffect() from the limma package.
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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32 Finally, dimenson reduction such as PCA or UMAP (on the PCA components) is provided. PCA and UMAP plots are then provided alongside with the (optional) quality controls plots within the `Plots` collection.
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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34 Final log2 transformed, normalized, imputed and batch-corrected data are provided, with the option to export also intermediate results.
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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36 Due to the internal complexity of data formats handling, we opted for one form with pre-defined settings for the whole processing pipeline. However, we highly recommend to check also QC plots and intermediate results and based on that adjust the workflow settings.
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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37 </token>
cd2f3a280463 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b
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38 </macros>