## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library(BUSpaRse) library(BSgenome.Hsapiens.UCSC.hg38) library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(EnsDb.Hsapiens.v86) ## ----------------------------------------------------------------------------- # For Drosophila dl_transcriptome("Drosophila melanogaster", out_path = "fly", gene_biotype_use = "cellranger", verbose = FALSE) list.files("fly") ## ----------------------------------------------------------------------------- dl_transcriptome("Caenorhabditis elegans", out_path = "worm", verbose = FALSE, gene_biotype_use = "cellranger", ensembl_version = 97) list.files("worm") ## ----------------------------------------------------------------------------- dl_transcriptome("Saccharomyces cerevisiae", out_path = "yeast", type = "fungus", gene_biotype_use = "cellranger", verbose = FALSE) list.files("yeast") ## ----------------------------------------------------------------------------- # Specify other attributes tr2g_mm <- tr2g_ensembl("Mus musculus", ensembl_version = 99, other_attrs = "description", gene_biotype_use = "cellranger") ## ----------------------------------------------------------------------------- head(tr2g_mm) ## ----------------------------------------------------------------------------- # Plants tr2g_at <- tr2g_ensembl("Arabidopsis thaliana", type = "plant") ## ----------------------------------------------------------------------------- head(tr2g_at) ## ----------------------------------------------------------------------------- # Subset of a real Ensembl FASTA file toy_fasta <- system.file("testdata/fasta_test.fasta", package = "BUSpaRse") tr2g_fa <- tr2g_fasta(file = toy_fasta, write_tr2g = FALSE, save_filtered = FALSE) head(tr2g_fa) ## ----------------------------------------------------------------------------- # Subset of a reral GTF file from Ensembl toy_gtf <- system.file("testdata/gtf_test.gtf", package = "BUSpaRse") tr2g_tg <- tr2g_gtf(toy_gtf, Genome = BSgenome.Hsapiens.UCSC.hg38, gene_biotype_use = "cellranger", out_path = "gtf") head(tr2g_tg) ## ----------------------------------------------------------------------------- list.files("gtf") ## ----------------------------------------------------------------------------- tr2g_hs <- tr2g_TxDb(TxDb.Hsapiens.UCSC.hg38.knownGene, get_transcriptome = FALSE, write_tr2g = FALSE) head(tr2g_hs) ## ----------------------------------------------------------------------------- tr2g_hs86 <- tr2g_EnsDb(EnsDb.Hsapiens.v86, get_transcriptome = FALSE, write_tr2g = FALSE, gene_biotype_use = "cellranger", use_gene_version = FALSE, use_transcript_version = FALSE) head(tr2g_hs86) ## ----------------------------------------------------------------------------- sessionInfo()