recipe bioconductor-busparse

kallisto | bustools R utilities

Homepage

https://bioconductor.org/packages/3.11/bioc/html/BUSpaRse.html

License

BSD_2_clause + file LICENSE

Recipe

/bioconductor-busparse/meta.yaml

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.

package bioconductor-busparse

(downloads) docker_bioconductor-busparse

Versions

1.2.1-01.0.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-busparse

and update with:

conda update bioconductor-busparse

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-busparse:<tag>

(see bioconductor-busparse/tags for valid values for <tag>)