# kallisto | bustools R utilities

## Documentation for package ‘BUSpaRse’ version 1.4.2

- 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