Package: BUSpaRse 1.19.0
Lambda Moses
BUSpaRse: kallisto | bustools R utilities
The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Here biotypes can be filtered and scaffolds and haplotypes can be removed, and the filtered transcriptome can be extracted and written to disk. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices.
Authors:
BUSpaRse_1.19.0.tar.gz
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BUSpaRse.pdf |BUSpaRse.html✨
BUSpaRse/json (API)
NEWS
| # Install 'BUSpaRse' in R: |
| install.packages('BUSpaRse', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bustools/busparse/issues
- cellranger_biotypes - Cell Ranger gene biotypes
- 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
- refseq_gff_mcols - Tags in the attributes field of RefSeq GFF files
On BioConductor:BUSpaRse-1.19.0(bioc 3.20)BUSpaRse-1.18.0(bioc 3.19)
Last updated 2 months agofrom:1bebbb0ae6
Exports:annots_from_fa_dfannots_from_fa_GRangesdl_transcriptomeEC2geneget_inflectionget_knee_dfget_velocity_filesknee_plotmake_sparse_matrixread_count_outputread_velocity_outputsave_tr2g_bustoolssort_tr2gspecies2datasetsubset_annottr2g_EnsDbtr2g_ensembltr2g_fastatr2g_gff3tr2g_gtftr2g_TxDbtranscript2gene
Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrensembldbfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrangespngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppProgressRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryamlzeallotzlibbioc
