https://github.com/rptashkin/tcga_mirnaseq_matrix
miRNAseq data matrix from downloaded TCGA data
https://github.com/rptashkin/tcga_mirnaseq_matrix
Last synced: 24 days ago
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miRNAseq data matrix from downloaded TCGA data
- Host: GitHub
- URL: https://github.com/rptashkin/tcga_mirnaseq_matrix
- Owner: rptashkin
- License: gpl-3.0
- Created: 2015-07-29T02:06:00.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2019-03-26T18:36:16.000Z (about 6 years ago)
- Last Synced: 2025-05-12T14:15:51.027Z (24 days ago)
- Language: R
- Homepage:
- Size: 43.9 KB
- Stars: 8
- Watchers: 3
- Forks: 9
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# TCGA_miRNASeq_matrix
This repository will contain support scripts and files to generate a matrix file using miRNASeq data downloaded from TCGA (https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm)
The R code "get_mature_miR_matrix.R" in conjunction with the lookup txt file "hsa_miR_accessionTOname.txt" may be used to convert individual sample isoform level miRNA RNA-seq data (downloaded via TCGA Data Matrix data portal) to a matrix file for all samples, using mature miRNA names. There are two main outputs for this code:
1) A *sumSort.txt file for each sample *isoform.quantification.txt file. This file collapes to mature miRNA names and provides the sum of the read_count for all miRNA_region IDs that map to a give mature miRNA.
2) The final output: "miR_counts_matrix.txt". This file is a matrix file of each sumSort.txt file generated earlier in the script.