Man pages for lambdamoses/BUStoolsR
kallisto | bustools R utilities

annot_circularTransfer information about circular chromosomes between...
annots_from_fa_dfGet genome annotation from Ensembl FASTA file
cellranger_biotypesCell Ranger gene biotypes
check_char1Check that an object is a character vector of length 1
check_genomeCheck for chromosomes in genome but not annotation
check_gffCheck inputs to tr2g_gtf and tr2g_gff3
check_tag_presentCheck that a tag is present in attribute field of GTF/GFF
check_txCheck if transcript ID in transcriptome and annotation match
dl_transcriptomeDownload transcriptome from Ensembl
dot-get_velocity_filesGenerate RNA velocity files for GRanges
EC2geneMap EC Index to Genes Compatible with the EC
ensembl_gene_biotypesGene biotypes from Ensembl
ensembl_gff_mcolsThese are the column names of the 'mcols' when the Ensembl...
ensembl_gtf_mcolsTags in the attributes field of Ensembl GTF files
ensembl_tx_biotypesTranscript biotypes from Ensembl
get_intron_flanksGet flanked intronic ranges
get_velocity_filesGet files required for RNA velocity with bustools
knee_plotPlot the transposed knee plot and inflection point
make_sparse_matrixConvert the Output of 'kallisto bus' into Gene by Gell Matrix
match_styleMatch chromosome naming styles of annotation and genome
read_count_outputRead matrix along with barcode and gene names
read_velocity_outputRead intronic and exonic matrices into R
refseq_gff_mcolsTags in the attributes field of RefSeq GFF files
save_tr2g_bustoolsSave transcript to gene file for use in 'bustools'
sort_tr2gSort transcripts to the same order as in kallisto index
species2datasetConvert Latin species name to dataset name
standardize_tagsStandardize GRanges field names
sub_annotRemove chromosomes in anotation absent from genome
subset_annotSubset genome annotation
tr2g_EnsDbGet transcript and gene info from EnsDb objects
tr2g_ensemblGet transcript and gene info from Ensembl
tr2g_fastaGet transcript and gene info from names in FASTA files
tr2g_gff3Get transcript and gene info from GFF3 file
tr2g_GRangesGet transcript and gene info from GRanges
tr2g_gtfGet transcript and gene info from GTF file
tr2g_junctiontr2g for exon-exon junctions
tr2g_TxDbGet transcript and gene info from TxDb objects
transcript2geneMap Ensembl transcript ID to gene ID
validate_velocity_inputValidate input to get_velocity_files
write_velocity_outputWrite the files for RNA velocity to disk
lambdamoses/BUStoolsR documentation built on Jan. 31, 2024, 5:11 a.m.