allensdk.internal.pipeline_modules.gbm.generate_gbm_heatmap module

allensdk.internal.pipeline_modules.gbm.generate_gbm_heatmap.create_gene_fpkm_table(analysis_run_records)

Creates a a matrix (“rows x columns = genes x samples”) of fpkm gene expression values for each particular (gene, sample) pair. Rows are sorted by entrez_id and columns are by rna_well_id

allensdk.internal.pipeline_modules.gbm.generate_gbm_heatmap.create_genes_for_transcripts(analysis_run_transcript_file)

Creates a list that contains the associated gene for each transcript sorted alphabetically

allensdk.internal.pipeline_modules.gbm.generate_gbm_heatmap.create_sample_metadata(sample_metadata_records)

Creates a table of sample metadata sorted by rna_well_id

allensdk.internal.pipeline_modules.gbm.generate_gbm_heatmap.create_transcript_fpkm_table(analysis_run_records)

Creates a a matrix (“rows x columns = transcripts x samples”) of fpkm gene expression values for each particular (transcript, sample) pair. Rows are sorted by transcript id and columns are by rna_well_id

allensdk.internal.pipeline_modules.gbm.generate_gbm_heatmap.create_transcripts_for_genes(analysis_run_gene_file)

Creates a list that contains the associated transcript for each gene sorted by entrez_id

allensdk.internal.pipeline_modules.gbm.generate_gbm_heatmap.main()