HTOparser

Hash-tag oligo parsing functions for scRNA-seq data

Requirements

All requirements for HTOparser are available from CRAN, and should be installed automatically by install_github():

Imports:
    assertthat (>= 0.2.1),
    dplyr (>= 0.8.0.1),
    purrr (>= 0.3.2),
    R.utils (>= 2.8.0)
Depends:
    data.table (>= 1.12.2),
    Matrix (>= 1.2-17)

Installation

This package can be installed from Github using the devtools package.

R -e 'install.packages("HTOparser", type = "source", repos = NULL)'

Test Data

This package includes test datasets that can be used for writing tests, vignettes, or demos. These files are stored in /inst/testdata/.

CITE-seq-Count

Data generated using CITE-seq-Count can be loaded using:

library(HTOparser)

test_hto_table <- fread(system.file("testdata/CITE-seq_count_matrix.csv.gz",
                                    package = "HTOparser"))
test_hto_mat <- as(as.matrix(test_hto_table[1:11,-1]), "dgCMatrix")

Row names of this matrix can be converted to barcodes using:

test_hto_key <- fread(system.file("testdata/CITE-seq_count_tags.csv",
                                  package = "HTOparser"),
                      header = FALSE)

rownames(test_hto_mat) <- test_hto_key$V1[match(test_hto_table[[1]][1:11], test_hto_key$V2)]

awk-based results

A table of results from awk-based parsing of HTO FASTQ files can be loaded using:

library(data.table)

test_hto_table <- fread(system.file("testdata/awk_pipeline_counts_table.csv.gz",
                                    package = "HTOparser"))
colnames(test_hto_table) <- c("count","cell_barcode","hto_barcode")

BioLegend TotalSeq References

CSV files with reference information for the TotalSeqA Hash Tag Oligo sequences are stored in /inst/data/, and have convenient wrapper functions to make them easy to load:

human_totalseq_ref <- totalseq_a_human()
mouse_totalseq_ref <- totalseq_a_mouse()
biotin_totalseq_ref <- totalseq_a_biotin()

Tests

Tests for HTOparser are implemented using the testthat testing suite:
https://testthat.r-lib.org/

To run tests for this package, download the repository from Github and run devtools::test() in R from the base directory of the package.

Extra-stringent, CRAN-level package testing can be performed using devtools::check() in R.

Style and Standards

This package aims to conform to the tidyverse style guide:
https://style.tidyverse.org/index.html

General information about R package conventions can be found in R Packages:
http://r-pkgs.had.co.nz/

Legal Information

License

The license for this package is available on Github in the file LICENSE.txt in this repository.

Level of Support

We are not currently supporting this code, but simply releasing it to the community AS IS but are not able to provide any guarantees of support. The community is welcome to submit issues, but you should not expect an active response.

Contribution Agreement

If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in the file CONTRIBUTING.md in this repository.