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build_coexp_direct_network()
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Build Direct Co-Expression network |
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build_coexp_intra_study_spearman_network()
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Build Co-exp network for each study and average |
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date_code()
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create date code of the form YYYYMMDD
inputs:
d (optional): date code in the format of Sys.Date() for which to generate the date code, defaulting to 'today' |
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download_expression_data()
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Download RNA-Seq expression runs from SRA |
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estimate_expression()
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Estimate expression data from SRA run and reference genome |
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gather_estimated_expression()
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Gather estimated expression data for analysis |
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gather_estimated_expression_meta()
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Gather estimated expression data metadata |
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get_deepfri_predictions()
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Use the DeepFRI webserver to get sequence and structure based gene function prediction |
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get_sra_connection()
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Get connection to the sequence read archive database |
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load_parameters()
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Load parameters |
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network_gba()
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Evaluate network Guilt By Association and report AUROC scores |
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plot_network_heatmap()
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Plot network heatmap |
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prepare_reference_genome()
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Use RSEM to prepare reference genome |
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propagate_go_annotations()
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Propagate GO term annotations |
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read_biogrid_tab2()
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parse BioGRID tab2 format |
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retrieve_sra_runs()
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Retrieve SRA runs from the SRAmeta database |
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submit_estimate_expression_slurm()
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Submit estimate gene expression job to SLURM cluster |
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validate_downloaded_runs()
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Check that the downloaded runs are not corrupted |
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validate_estimated_expression()
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Validate estimated expression runs |