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Hours: 178.60

Date User Activity Issue Comment Hours
11/12/2019 Thys Potgieter Development Feature #104: Summary table of mRNA and proteomics analysis for identified gene targets, protein level mean abundance per group added. Latest mRNA data integrated, proteomics average intensity added, addition of InterProScan and KO annotations, tables generated 3.00 Actions
11/12/2019 Thys Potgieter Development Feature #103: Median group intensity added to output for visualization of proteomics target expression profiles Median iBAQ intensity added to summary table, unit-tests added 3.00 Actions
10/28/2019 Thys Potgieter Analysis Feature #104: Summary table of mRNA and proteomics analysis for identified gene targets, protein level mean abundance per group added. Mean protein abundance added to pipeline output. Started on integrating mRNA in summary table. 2.00 Actions
10/04/2019 Jon Ambler Analysis Support #90: QC of aligned reads 2.00 Actions
10/04/2019 Jon Ambler Analysis Support #100: Time seres analysis 24.00 Actions
10/04/2019 Jon Ambler Analysis Support #100: Time seres analysis 16.00 Actions
10/04/2019 Jon Ambler Analysis Support #92: Differential expression analysis 16.00 Actions
09/18/2019 Thys Potgieter Analysis Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization different normalization and imputation techniques tested - Median, Quantile, and None compared. Slides generated. Median better than Quantile, KNN appears better than BPCA for gene set enrichment but not protein differential abundance 4.00 Actions
09/17/2019 Thys Potgieter Analysis Feature #98: Sample processing with MetaMorpheus Sample Calibration run with MetaMorpheus 2.00 Actions
09/17/2019 Thys Potgieter Analysis Feature #98: Sample processing with MetaMorpheus Pilot run with 4 samples 2.00 Actions
08/08/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Contaminant versus total protein content visualization figure (Added to QC component of pipeline) 2.00 Actions
08/05/2019 Thys Potgieter Analysis Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Runs for cells and tissues completed, QC figures added to meeting presentation, output moved to research drive. 3.00 Actions
08/05/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Gene and protein ID added to differential abundance analysis output, unit tests. 3.00 Actions
07/25/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Exclude samples from downstream analysis using config file 2.00 Actions
07/23/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Boxplots for peptide identifications, scatterplots of sample protein intensities against median (QC). 4.00 Actions
07/19/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Bayes PCA tested, configurable normalization method in pipeline. Box plots improved to exclude outliers in plots 4.00 Actions
07/02/2019 Jon Ambler Investigation Support #90: QC of aligned reads 3.00 Actions
07/02/2019 Jon Ambler Analysis Support #92: Differential expression analysis 6.00 Actions
07/02/2019 Thys Potgieter Analysis Support #86: Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu Methods summary presentation created and sent to Relebohile 2.00 Actions
07/02/2019 Thys Potgieter Development Support #86: Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu Data analyzed, experimental design file created for cells and tissues separately. 2.00 Actions
07/02/2019 Thys Potgieter Development Support #86: Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu Bug fixes and unit tests for mqmetaproteomics pipeline 6.00 Actions
07/02/2019 Thys Potgieter Analysis Support #86: Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu Quality control - samples less than 1 percent assigned spectra excluded. normalization and imputation methods tested. 6.00 Actions
07/02/2019 Thys Potgieter Analysis Support #85: MaxQuant run of raw proteomics data MaxQuant run restarted, experiment names added 2.00 Actions
06/24/2019 Jon Ambler Development Support #92: Differential expression analysis Creating the design_formula file needed to create DESeqDataSet 5.00 Actions
06/24/2019 Jon Ambler Development Support #92: Differential expression analysis Sample gene counts need to be merged 6.00 Actions
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