Installation
About
Wrapper around various existing tools and command-line interfaces, providing a standard interface, simple parallelization, and detailed logging. For microarray data, maps probe sets to standard gene IDs, building on 'GEOquery' Davis and Meltzer (2007) doi:10.1093/bioinformatics/btm254, 'ArrayExpress' Kauffmann et al. (2009) doi:10.1093/bioinformatics/btp354, Robust multi-array average 'RMA' Irizarry et al. (2003) doi:10.1093/biostatistics/4.2.249, and 'BrainArray' Dai et al. (2005) doi:10.1093/nar/gni179. For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and quality trimming using 'TrimGalore' Krueger
seeker.hugheylab.org | |
github.com/hugheylab/seeker |
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Depends
R | ≥ 3.5 |