COSMIC provides a simple interface for downloading data files. the URL from the JSON snippet and make a request to that URL to download the data file:
q = files() %>% GenomicDataCommons::select(available_fields('files')) %>% filter(~ cases.project.project_id == 'TCGA-GBM' & data_type == 'Aligned Reads' & experimental_strategy == 'RNA-Seq' & data_format == 'BAM') file_ids = q %>% response… Download: select one of the options from the drop down list to download the figure (as a PNG or SVG image), the data (as a text file or in JSON format), or the results of the statistical analysis (as a text file or in JSON format). You can use the log file integrity (LFI) validation as a part of your IT security and auditing processes. Google Summer of Code Open Health GDC exploration (NCI's Genomic Data Commons) - mathbiol/gdcfun Contribute to OpenGenomics/pancan-maf-merge development by creating an account on GitHub.
You can use the log file integrity (LFI) validation as a part of your IT security and auditing processes. Google Summer of Code Open Health GDC exploration (NCI's Genomic Data Commons) - mathbiol/gdcfun Contribute to OpenGenomics/pancan-maf-merge development by creating an account on GitHub. Scripts used in GGP work. Contribute to pihltd/ISB-CGC-Pipelines development by creating an account on GitHub. Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R - sbg/sevenbridges-r Integration of GDCWebApp service in Galaxy as an asynchronous Data Source - fabio-cumbo/GDCWebApp4Galaxy Repository for the NCI Cloud Pilot Workshop on May 24-25, 2016 - sbg/nci-workshop
The data files represented here includes data available in the Human Protein Atlas version 19.1. 20, RNA TCGA cancer sample gene data gene set using the search function (via the Download: Custom TSV/JSON link on the result page). In order to download data from TCGA data portal: 1. If you need RAW data such as FASTQ files you have find level 1 data, but often this kind of data is not This is where we attempt to characterize chromosomal instability in colorectal cancer. - dampierch/aneuploidy A common pancancer command line interface. Contribute to ICGC-TCGA-PanCancer/cli development by creating an account on GitHub. This tool is intended to be a generic upload script to be used to upload VCF's into GNOS. Despite the name, this tool can be used to download bam files (i.e. neither handle vcfs or upload anything). - ICGC-TCGA-PanCancer/vcf-uploader Loads TCGA data into NDEx. Contribute to ndexcontent/ndextcgaloader development by creating an account on GitHub. A playbook that sets up sensu client+ server and other tools such as logstash - ICGC-TCGA-PanCancer/monitoring-bag
Dockerfile for loader docker container. Includes uAIMLoader and ImageLoader. - camicroscope/LoaderDockerContainer A step to step guide on mining cancer biomarker based on microRNA data and tissue specificity of disease) + Molecular Pathway Investigation - stefanuswibowo/miTS_Pathway GridVar is a jQuery plugin that visualizes multi-dimensional datasets as layers organized in a row-column format. - Novartis/gridvar The “bidirectional gene pair” indicates a particular head-to-head gene organization in which transcription start sites of two genes are located on opposite strands of genomic DNA within a region of one kb. q = files() %>% GenomicDataCommons::select(available_fields('files')) %>% filter(~ cases.project.project_id == 'TCGA-GBM' & data_type == 'Aligned Reads' & experimental_strategy == 'RNA-Seq' & data_format == 'BAM') file_ids = q %>% response… Download: select one of the options from the drop down list to download the figure (as a PNG or SVG image), the data (as a text file or in JSON format), or the results of the statistical analysis (as a text file or in JSON format).
verbose. If TRUE it will print a message of where the file is being downloaded to. For TCGA we acquired metadata information from 3 different sources: GDC: via a json query. CGC: via json queries and a custom script to merge the tables.
