Scripts to analyze differential fractionation (DIF-FRAC) experiments. Compares two elut files for significant changes between conditions.
Primary script to compare experiments
Plotting script to visualize changes in elutions across experiments
Size exclusion chromatography (SEC) fractionation experiment on mouse embryonic stem cells with no treatment (control)
Size exclusion chromatography (SEC) fractionation experiment on mouse embryonic stem cells with RNase A treatment
Annotation file for identifying known RNA binding proteins, most annotations are from Hentze et al. Nat Rev Mol Cell Biol. 2018
python diffrac.py --elution_files ./data/MES_SEC_Cntl_20180601.prot_count_mFDRpsm001.elut ./data/MES_SEC_RNAse_20180601.prot_count_mFDRpsm001.elut --features diffrac diffrac_percent pearsonr diffrac_normalized mean_abundance emd zscore sliding_zscore fdr_correct sliding_fdr_correct --output_file MES_SEC_Cntl_RNAse_20180601_diffrac_features.feat --annotated_list ./data/mouse_rna_annotations_go_uniprot_hentze.txt --use_gmm &> MES_SEC_Cntl_RNAse_diffrac_feat.out
python evaluation/plots/plot_sparklines.py --filenames ./data/MES_SEC_Cntl_20180601.prot_count_mFDRpsm001.elut ./data/MES_SEC_RNAse_20180601.prot_count_mFDRpsm001.elut --proteins P35601 Q9WUK4 Q8R323 Q99J62 Q9D0F6 --output_filename ./RFC_sparklines.pdf --labels Control RNAseA --parse_fraction_name cell_type col_type condition fraction subindex date --annotation_file ./data/uniprot-proteome_mouse_annotations_20180331.csv --annotation_file_sep , --id_column genename
Additional script for comparing experiments.
python diff_abun_zscore.py [# of replicates] [method for z-score collapse] [control elut file] [treatment elut file]
python diff_abun_zscore.py 1 stouffer ./data/MES_SEC_Cntl_20180601.prot_count_mFDRpsm001.elut ./data/MES_SEC_RNAse_20180601.prot_count_mFDRpsm001.elut
Thanks to Ben Liebeskind (@bliebeskind) for elution file reader code.