MIRSORT_ANNOTATION_DF.json

{
    "assemble_anndata.py":{
        "expression_file": "<PATH>/preprocessed/expression_mat/raw_count__sequences.txt",
        "obs_file": "<PATH>/preprocessed/0_info/sample_info.txt",
        "ad_path": "miRSort_combined__ngs-23.11.0.h5ad",
        "version": "23.11.0",
        "fasta_path": "<PATH>/preprocessed/expression_mat/features_all_sequences.fa"
    },
    "merge_sRNAclass_annotations.py":{
        "unitas_annot_path": "unitas_annotation/UNITAS_dd-mm-yyyy_features_detected_sequences__publication.fa_#1/unitas.full_annotation_matrix_justannoseqs.txt",
        "sports_annot_path": "sports_annotation/1_features_detected_sequences__publication/features_detected_sequences__publication_result/features_detected_sequences__publication_output_justannoseqs.txt",
        "snoDB_annot_path": "snoDB.fa",
        "sRNA_class_annot_path": "sRNA_class_annotation.csv"
    },
    "rRNA_position_classification.py":{
        "seq_path": "sports_annotation/1_features_detected_sequences__publication/features_detected_sequences__publication_fa/",
        "ref_path": "Homo_sapiens/rRNAdb/",
        "rRNA_name_annot_path": "sports_annotation/rRNA_start_pos_binned.csv",
        "YRNA_name_annot_path": "sports_annotation/YRNA_start_pos_binned.csv"
    },
    "generate_sRNA_sub_class_annotation_df.py":{
        "snoDB_info_path": "snoDB.tsv",
        "sRNA_sub_class_annot_path": "sRNA_class_subtypes_annot__miRSort_combined.csv"
    },
    "create_seq_annotation_df.py":{
        "ANNOTATION_DF": "miRSort_combined_ANNO_DF_230120.csv"
    },  
    "ad_reduce_features.py":{
        "version": "23.11.1",
        "ad_reduced_path": "miRSort_combined__ngs-23.11.1.h5ad"
    },
    "ad_aggregate.py":{
        "ad_seq_path": "",
        "ad_seq_filename": "miRSort_combined__ngs-23.11.1.h5ad",
        "ad_aggregated_path": "",
        "ad_aggregated_filename": "miRSort_combined__ngs_aggregated-23.11.1.h5ad"
    },
    "ad_reduce_features_further.py":{
        "ad_aggregated_bloodcomponents_path": "miRSort_combined__ngs_aggregated-23.11.1__celltypes.h5ad",
        "ad_aggregated_wholeblood_path": "miRSort_combined__ngs_aggregated-23.11.1__whole_blood.h5ad"
    },
    "ad2csv.py":{
        "tsne_path": "miRSort_combined__ngs_aggregated-23.11.1__tsne_embedding_data.csv",
        "obs_path": "miRSort_combined__ngs_aggregated-23.11.1__obs_data.csv",
        "GEO_smp_record_info": "miRSort_combined__ngs_aggregated-23.11.1__GEO_smp_record_info.csv",
        "sRNAtype_path": "miRSort_combined__ngs_aggregated-23.11.1__sRNAtype_data.csv",
        "sRNA_subtype_path": "miRSort_combined__ngs_aggregated-23.11.1__sRNA_subtype_data.csv",
        "expr_path": "miRSort_combined__ngs_aggregated-23.11.1__log2RPM+1_expression_data.csv",
        "expr_extra_path": "miRSort_combined__ngs_aggregated-23.11.1__log2RPM+1_WHOLEBLOOD_expression_data.csv",
        "box_path": "miRSort_combined__ngs_aggregated-23.11.1__boxplot_data.csv",
        "sRNA_aggreg_path": "miRSort_combined__ngs_aggregated-23.11.1__sRNA_aggreg_prop_data.csv",
        "expr_mean_path": "miRSort_combined__ngs_aggregated-23.11.1__log2RPM+1_mean_data.csv",
        "marker_path": "miRSort_combined__ngs_aggregated-23.11.1__celltype_marker_data.json",
        "cell_prop_path": "miRSort_combined__ngs_aggregated-23.11.1__cell_prop_data.csv",
        "RPM_mean_path": "miRSort_combined__ngs_aggregated-23.11.1__RPM_mean_data.csv",
        "scaled_prop_path": "miRSort_combined__ngs_aggregated-23.11.1__proportional_scaled_RPM_mean_data.csv",
        "corr_path": "miRSort_combined__ngs_aggregated-23.11.1__bloodcount_correlation_data.csv",
        "tsne_plot_all_path": "miRSort_combined__ngs_aggregated-23.11.1__tSNE_plot_all.pdf",
        "tsne_plot_filtered_path": "miRSort_combined__ngs_aggregated-23.11.1__tSNE_plot_filtered.pdf",
        "counts_plot_path": "miRSort_combined__ngs_aggregated-23.11.1__counts_plot_filtered.pdf",
        "FA_plot_path": "miRSort_combined__ngs_aggregated-23.11.1__FA_ratio_plot_filtered.pdf",
        "suppl_table_1_path": "miRSort_combined__ngs_aggregated-23.11.1__suppl_table_1_data.csv",
        "suppl_table_2_path": "miRSort_combined__ngs_aggregated-23.11.1__suppl_table_2_data.csv",
        "suppl_table_3_path": "miRSort_combined__ngs_aggregated-23.11.1__suppl_table_3_data.csv"
    },
    "compare_2_Juzenas.py":{
        "output_folder": "compare2Kiel/",
        "Kiel_ad_path": "Kiel_miRNA_log2RPM.h5ad"   
    }
}