download_bacterial_transcripts: Download the entire ENSEMBL transcript DB for bacteria.

In Gibbons-Lab/mbtools: Provides helper functions for microbiome preprocessing and analysis

Download the entire ENSEMBL transcript DB for bacteria.

Description

Download the entire ENSEMBL transcript DB for bacteria.

Usage

download_bacterial_transcripts(
  out = "transcripts",
  what = "cdna",
  np = 8,
  remove_redundant = TRUE
)

Arguments

out	Where to store the downloaded transcript files.
what	Download in which format. Can be "cdna" or "protein" to download reverse transcribed DNA (cDNA) or protein sequences.
np	How many parallel download processes to use.
remove_redundant	Whether to remove alternative assemblies for the same strain.

Value

A data table containing the downloaded species and assemblies.

Gibbons-Lab/mbtools documentation built on Jan. 28, 2024, 11:08 a.m.