ArchR_utilies

R functions for a few common purposes:

• amend UCSC GTF files by adding entries for genes
• split a multi-fasta file for a genome assembly into per-chromosome single fasta files
• automatically generate a seed file for forging a BSgenome package
• forge a BSgenome package from a directory containing single fasta files for individual chromosomes of a genome assembly using the seed file
• check, build and install the BSgenome package
• forge a TxDb database from a GTF file
• get gene IDs and gene symbols from the GTF file or query Biomart databases
• create geneAnnotation and genomeAnnotation for ArchR-based analysis of scATAC-seq data
• forge a OrgDb package from a dataframe containing gene IDs and gene symbols