browseRC: Browse a gene on Ribocrypt webpage
In Miswi/RiboCrypt: Interactive visualization in genomics

browseRC

R Documentation

Browse a gene on Ribocrypt webpage

Description

Can also disply local RiboCrypt app

Usage

browseRC(
  symbol = NULL,
  gene_id = NULL,
  tx_id = NULL,
  exp = "all_merged-Homo_sapiens_modalities",
  libraries = NULL,
  leader_extension = 0,
  trailer_extension = 0,
  viewMode = FALSE,
  other_tx = FALSE,
  plot_on_start = TRUE,
  frames_type = "columns",
  kmer = 1,
  host = "https://ribocrypt.org",
  browser = getOption("browser")
)

Arguments

`symbol`	gene symbol, default NULL
`gene_id`	gene symbol, default NULL
`tx_id`	gene symbol, default NULL
`exp`	experiment name, default "all_merged-Homo_sapiens_modalities"
`libraries`	NULL, default to first in experiment, c("RFP","RNA") would add RNA to default.
`leader_extension`	integer, default 0. (How much to extend view upstream)
`trailer_extension`	integer, default 0. (How much to extend view downstream)
`viewMode`	FALSE (transcript view), TRUE gives genomic.
`other_tx`	FALSE, show all other annotation in region (isoforms etc.)
`plot_on_start`	logical, default TRUE. Plot gene when opening browser.
`frames_type`	"columns"
`kmer`	integer, default 1 (no binning), binning size of windows, to smear out the signal.
`host`	url, default "https://ribocrypt.org". Set to localhost for local version.
`browser`	getOption("browser")