rmadupuri
/ explore_master_anndata_object.ipynb
Last active
September 22, 2025 20:35
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rmadupuri
/ add_TBL_scores.py
Last active
November 15, 2024 16:30
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| #Script to integrate TBL scores to Pancan, CCLE, PACAWG clinical_sample files | |
| import os | |
| import pandas as pd | |
| dh_path = "/Users/madupurr/Github/datahub/public" | |
| tbl_scores_path = "/Users/madupurr/Desktop/TBL_scores/TBL_scores.txt" | |
| tbl_scores = pd.read_csv(tbl_scores_path ,sep='\t',header = None) |
rmadupuri
/ add_genie_prefix_to_pats_samples.py
Created
August 9, 2024 16:14
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| import sys | |
| import os | |
| study_dir = "/Users/madupurr/Desktop/genie_subset/impact_subset" | |
| output_dir = "/Users/madupurr/Desktop/genie_subset/corrected_ids" | |
| files = os.listdir(study_dir) | |
| def extract_header(study_dir, filename): | |
| with open(study_dir+'/'+filename, 'r') as infile: |
rmadupuri
/ htan_crc_merge_3_h5ad_files_generate_absolute_relative_freq_bulk_rna_counts.ipynb
Created
April 29, 2024 13:18
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rmadupuri
/ htan_crc_merge_2_h5ad_files_generate_absolute_relative_freq_bulk_rna_counts.ipynb
Created
October 5, 2023 12:16
# This script merges two h5ad files and generates # 1. The absolute and relative cell frequencies # 2. Pseudo bulk RNA counts per samples averaged across the cells.
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rmadupuri
/ remove-duplicate-maf-variants.py
Created
August 9, 2023 12:27
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| #!/usr/bin/python | |
| import sys | |
| import os | |
| import optparse | |
| # Script to remove duplicate maf records based on the 8 key columns. | |
| # Calculates VAF for each record and picks the record with high VAF | |
| # Formula for VAF = t_alt_count / (t_ref_count + t_alt_count) | |
| ERROR_FILE = sys.stderr |
rmadupuri
/ filter_idh_tert_variants.ipynb
Last active
September 14, 2023 19:37
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rmadupuri
/ process_pass_anno.ipynb
Last active
September 14, 2023 16:13
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rmadupuri
/ process_pass_geno.ipynb
Last active
September 14, 2023 15:42
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rmadupuri
/ convert_3d_matrix.py
Last active
September 13, 2023 18:25
Convert tabular data to a 3D matrix
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| """Convert data in | |
| python code to convert | |
| P-0000246-T05 LTB 2 | |
| P-0000246-T05 NOTCH4 2 | |
| P-0002556-T03 KMT2A 2 | |
| P-0003309-T02 ATM -2 | |
| to | |
| Gene P-0000246-T05 P-0002556-T03 P-0003309-T02 |
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