# kallisto | bustools R utilities

## Documentation for package ‘BUSpaRse’ version 1.1.1

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

## Help Pages

.get_velocity_files | Generate RNA velocity files for GRanges
annot_circular | Transfer information about circular chromosomes between genome and annotation
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
EC2gene | Map EC Index to Genes Compatible with the EC
get_intron_flanks | Get flanked intronic ranges
get_velocity_files | Get files required for RNA velocity with bustools
get_velocity_files-method | Get files required for RNA velocity with bustools
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
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