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Releases: vizkidd/R-COMPLETE

Data Extraction v1.0

07 Sep 12:25
@vizkidd vizkidd
v1.0-alpha
88439cd
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Data Extraction v1.0 Pre-release
Pre-release

!!IMPORTANT!!

  • Download Source Code
  • Kindly review and update "paramters.txt" before execution
  • ONLY RUN one instance of the pipeline - Check documentation for code examples to start the pipeline
  • CHECK list of dependencies

Dependencies: R

BiocManager::install("biomartr","dplyr","biomaRt","parallel","tools","RCurl","curl","purrr","fs","processx","ps","stringi","data.table","stringr","seqinr","GenomicRanges","rtracklayer","Rgb","bedr","tictoc")

Dependencies: Shell

sudo apt-get install bedtools samtools gzip parallel r-base

Details:

  • Script files for downloading and extracting data (including paramters.txt)
  • Requires a gene list
  • Optional: User list of genomes and GTFs (example provided)

Usage:

Rscript COMPLETE-data_extraction.R genelist.txt

Full Changelog: https://github.com/vizkidd/mrna_zipcodes/commits/main

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