kallisto | bustools R utilities

---

Documentation for package ‘BUSpaRse’ version 1.12.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

.get_velocity_files	Generate RNA velocity files for GRanges
annots_from_fa_df	Get genome annotation from Ensembl FASTA file
annots_from_fa_GRanges	Get genome annotation from Ensembl FASTA file
annot_circular	Transfer information about circular chromosomes between genome and annotation
cellranger_biotypes	Cell Ranger gene biotypes
check_char1	Check that an object is a character vector of length 1
check_genome	Check for chromosomes in genome but not annotation
check_gff	Check inputs to tr2g_gtf and tr2g_gff3
check_tag_present	Check that a tag is present in attribute field of GTF/GFF
check_tx	Check if transcript ID in transcriptome and annotation match
dl_transcriptome	Download transcriptome from Ensembl
EC2gene	Map EC Index to Genes Compatible with the EC
ensembl_gene_biotypes	Gene biotypes from Ensembl
ensembl_gff_mcols	These are the column names of the 'mcols' when the Ensembl GTF file is read into R as a 'GRanges', including 'gene_id', 'transcript_id', 'biotype', 'description', and so on, and the mandatory tags like 'ID', 'Name', and 'Parent'.
ensembl_gtf_mcols	Tags in the attributes field of Ensembl GTF files
ensembl_tx_biotypes	Transcript biotypes from Ensembl
get_inflection	Plot the transposed knee plot and inflection point
get_intron_flanks	Get flanked intronic ranges
get_knee_df	Plot the transposed knee plot and inflection point
get_velocity_files	Get files required for RNA velocity with bustools
get_velocity_files-method	Get files required for RNA velocity with bustools
knee_plot	Plot the transposed knee plot and inflection point
make_sparse_matrix	Convert the Output of 'kallisto bus' into Gene by Gell Matrix
match_style	Match chromosome naming styles of annotation and genome
read_count_output	Read matrix along with barcode and gene names
read_velocity_output	Read intronic and exonic matrices into R
refseq_gff_mcols	Tags in the attributes field of RefSeq GFF files
save_tr2g_bustools	Save transcript to gene file for use in 'bustools'
sort_tr2g	Sort transcripts to the same order as in kallisto index
species2dataset	Convert Latin species name to dataset name
standardize_tags	Standardize GRanges field names
subset_annot	Subset genome annotation
subset_annot-method	Subset genome annotation
sub_annot	Remove chromosomes in anotation absent from genome
tr2g_EnsDb	Get transcript and gene info from EnsDb objects
tr2g_ensembl	Get transcript and gene info from Ensembl
tr2g_fasta	Get transcript and gene info from names in FASTA files
tr2g_gff3	Get transcript and gene info from GFF3 file
tr2g_GRanges	Get transcript and gene info from GRanges
tr2g_gtf	Get transcript and gene info from GTF file
tr2g_junction	tr2g for exon-exon junctions
tr2g_TxDb	Get transcript and gene info from TxDb objects
transcript2gene	Map Ensembl transcript ID to gene ID
validate_velocity_input	Validate input to get_velocity_files
write_velocity_output	Write the files for RNA velocity to disk