File containing the implementation of Progenesis LFQ workflow for UPS1 dataset. (PDF 206 kb
Scripts detailed descriptions: command line arguments, output file descriptions and availability. (P...
Protein expression matrix. Protein expression matrix of raw data of 49 proteins/phosphoproteins assa...
All proteins identified in the qualitative proteome analysis. Supplemental qualitative proteome anal...
File containing the implementation of Progenesis LFQ workflow for Chlamydomonas-yeast dataset. (PDF ...
Figure S1. Scatterplots of the UPS1 dataset showing the position of the true positives and the true ...
Archive containing the R (version 3.4.4) implementation of the computational pipeline. (RAR 15 kb
Figure S3. Scatterplot of the yeast dataset showing the position of the true positives and the true ...
Figure S2. ROC curves comparison of using limma with or without robust regression in our pipeline wi...
Analysis simulated dataset 3. This simulated dataset models an input with incomplete annotation of c...
Figure S4. ROC curves comparison of using limma with or without robust regression in our pipeline wi...
Workflow for generating a simulated proteogenomic database for yeast. (DOCX 743Â kb
Normalization simulated dataset 3. The file contains the simulated datasets used to model difference...
Bioinformatic tools distribution. A. Peptimapper dockerfile. B. Workflow labeled “Peptimapper” avail...
Proportion of redundant peptides in decoy databases for simulated proteogenomic search. (DOCX 14Â kb
Supplementary methods. Descriptions on the human MS/MS data set, RNA sequencing analysis, constructi...
Scripts detailed descriptions: command line arguments, output file descriptions and availability. (P...
Protein expression matrix. Protein expression matrix of raw data of 49 proteins/phosphoproteins assa...
All proteins identified in the qualitative proteome analysis. Supplemental qualitative proteome anal...
File containing the implementation of Progenesis LFQ workflow for Chlamydomonas-yeast dataset. (PDF ...
Figure S1. Scatterplots of the UPS1 dataset showing the position of the true positives and the true ...
Archive containing the R (version 3.4.4) implementation of the computational pipeline. (RAR 15 kb
Figure S3. Scatterplot of the yeast dataset showing the position of the true positives and the true ...
Figure S2. ROC curves comparison of using limma with or without robust regression in our pipeline wi...
Analysis simulated dataset 3. This simulated dataset models an input with incomplete annotation of c...
Figure S4. ROC curves comparison of using limma with or without robust regression in our pipeline wi...
Workflow for generating a simulated proteogenomic database for yeast. (DOCX 743Â kb
Normalization simulated dataset 3. The file contains the simulated datasets used to model difference...
Bioinformatic tools distribution. A. Peptimapper dockerfile. B. Workflow labeled “Peptimapper” avail...
Proportion of redundant peptides in decoy databases for simulated proteogenomic search. (DOCX 14Â kb
Supplementary methods. Descriptions on the human MS/MS data set, RNA sequencing analysis, constructi...
Scripts detailed descriptions: command line arguments, output file descriptions and availability. (P...
Protein expression matrix. Protein expression matrix of raw data of 49 proteins/phosphoproteins assa...
All proteins identified in the qualitative proteome analysis. Supplemental qualitative proteome anal...
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