1) Added a feature_data table to synapse (https://www.synapse.org/#!Synapse:syn27644450) to make tracking of NMF indeces and features easier. This table can be loaded with the added function load_NMF_data() from the NMF_helper script.
2) The largest change is due to the mutational analysis updates. First, the PeCorA analysis scripts have been added, these are found in the PeCorA subfolder. Also, the script 11_raw_peptide_intensity.Rmd uploads a raw peptide intensity table to synapse (https://www.synapse.org/#!Synapse:syn27899073) for easy combination with the PeCorA result. Finally, there are some minor updates to the Over representation analysis and GSEA scripts, these now upload the raw enrichment results to synapse.
There are two changes changes on this PR:
1) Added a feature_data table to synapse (https://www.synapse.org/#!Synapse:syn27644450) to make tracking of NMF indeces and features easier. This table can be loaded with the added function load_NMF_data() from the NMF_helper script.
2) The largest change is due to the mutational analysis updates. First, the PeCorA analysis scripts have been added, these are found in the PeCorA subfolder. Also, the script 11_raw_peptide_intensity.Rmd uploads a raw peptide intensity table to synapse (https://www.synapse.org/#!Synapse:syn27899073) for easy combination with the PeCorA result. Finally, there are some minor updates to the Over representation analysis and GSEA scripts, these now upload the raw enrichment results to synapse.