https://www.nature.com/articles/s41467-018-07106-z
https://github.com/manutamminen/chlamy_proteome_evolution/blob/master/workflow.org
| File | Description |
|---|---|
| mqpar_v16.xml | MaxQuant configuration file (XML) |
| parameters.txt | MaxQuant configuration file (plain text) |
| proteinGroupsGoodColNames.csv | Proteomic data: output from MaxQuant |
| proteinGroups.txt | Proteomic data: output from MaxQuant including organelle hits |
| id_conversion_raw.txt | Conversion table for different database IDs |
| KEGG_Cp/annotation_table.csv | KEGG annotation table |
| KEGG_Chr/annotation_table_chr.csv | KEGG annotation table including organelle-encoded proteins |
| panther_annotations.csv | Panther annotation table |
| selected_clusters.csv | David annotation table |
| david_opposites.xlsx | David annotation table for the highly divergent proteins |
| circos/karyotype.txt | Circos configuration files |
| circos/circos.conf | |
| circos/colors_fonts_patterns.conf | |
| circos/housekeeping.conf | |
| circos/ideogram.conf | |
| circos/image.conf | |
| circos/ticks.conf | |
| ChlamEE_phenotypic_measurements.xlsx | Stoichiometry and respiration data |