| devodata {JMDplots} | R Documentation |
Data and chemical metrics for fruit fly and biofilm developmental proteomes.
getCBS17(metric, boot.R)
getFOK21(metric, boot.R)
metric |
character, name of metric (‘H2O’, ‘ZC’, or ‘length’) |
boot.R |
integer, number of bootstrap replicates |
getCBS17 calculates the weighted mean and bootstrap confidence interval for chemical metrics in the Drosophila melanogaster developmental proteome (Casas-Vila et al., 2017).
getFOK21 does the same for the Bacillus subtilis developmental proteome (Futo et al., 2021).
CBS+17_abundance.csv.xzProcessed protein abundance data from Supplemental Table S1 of Casas-Vila et al. (2017). Values in the columns for "imputed.log2.LFQ.intensity" were exponentiated, and means of all 4 replicates at each time point were taken to give the values in this file. Protein IDs were mapped to UniProt IDs in the "Entry" column.
CBS+17_aa.csv.xzAmino acid compositions obtained from the canonical UniProt sequences for all proteins.
CBS+17.R, CBS+17_mean_aa.csvR script and output for abundance-weighted mean amino acid compositions for proteins at each developmental time point.
FOK+21_abundance.csv.xzGene and protein abundance data from Supplementary File S10 of Futo et al. (2020). Values in the sheets named "TAI" and "PAI" were used without modification and stored in the columns starting with "T_" and "P_". Protein IDs were mapped to UniProt IDs in the "Entry" column.
FOK+21_aa.csv.xzAmino acid compositions obtained from the canonical UniProt sequences for all proteins.
FOK+21.R, FOK+21_mean_aa.csvR script and output for abundance-weighted mean amino acid compositions for proteins at each developmental time point.
Casas-Vilas N et al. (2017) The developmental proteome of Drosophila melanogaster. Genome Res. 27, 1273–1285. doi:10.1101/gr.213694.116
Futo M et al. (2021) Embryo-like features in developing Bacillus subtilis biofilms. Mol. Biol. Evol. 38, 31–47. doi:10.1093/molbev/msaa217
evdevH2O6 and evdevH2O7 are functions that use these files.
getCBS17()