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Transcriptome derived organismal aging clock
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lotrus28/ExpClock
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╔═══════════════════════════════════════════════════════════════════════════════════════════════╗ ║ ║ Minor errors might be present. Pay extra attention to passed arguments and hardcoded paths! ║ ║ To work with scripts you need to download these files from GTEx site: ║ - GTEx_Analysis_v6p_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.7z ║ - GTEx_Data_V6_Annotations_SampleAttributesDS.txt ║ - GTEx_Data_V6_Annotations_SubjectPhenotypesDS.txt ║ ║ Data division into testing and training sets is not supported yet. ╚═══════════════════════════════════════════════════════════════════════════════════════════════╝ = get_sign_features.sh Maaster bash script for separating data in tissue tables, finding significant features and evaluating them. The script is not optimized for parallel computation. You need to specify script-containing folder inside of this file = Scripts/ Contains scripts required by `get_sign_features.sh` = subj_sample_annot.txt Contains metadata available on GTEx samples: tissue, granular age and sex. The file is produced by './Scripts/join_sample_and_subj_annot.py from sample and subject annotations. = significant_features.txt 1st column: tissue 2nd column: Boruta confirmed features 3d column: Boruta tentative features The file is produced by './Scripts/boruta_clock.R' = tested_sign_features.txt Same as significant_features.txt but has 4 columns describing prediction quality: RMSE is root mean squere error and RSq is the fraction of variance explained. Some trees include only confirmed features and others — both confirmed and tentative.
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