Package: Isosceles

Title: Isoform Single-Cell and Long-read Expression Suite

Version: 0.2.1

Authors@R: c(

person("Michal", "Kabza", email = "[email protected]", role = c("aut", "cre")),

person("Tim", "Sterne-Weiler", email = "[email protected]", role = c("aut")))

Description: Transcript detection and quantification from long reads.

Depends:

R (>= 4.2.0),

SingleCellExperiment (>= 1.18.0)

Imports:

utils (>= 4.2.0),

methods (>= 4.2.0),

stats (>= 4.2.0),

rlang (>= 1.0.4),

assertthat (>= 0.2.1),

magrittr (>= 2.0.3),

tibble (>= 3.1.7),

tidyselect (>= 1.1.2),

dplyr (>= 1.0.9),

tidyr (>= 1.2.0),

forcats (>= 0.5.1),

glue (>= 1.6.2),

digest (>= 0.6.29),

Rcpp (>= 1.0.9),

Matrix (>= 1.4-1),

BiocParallel (>= 1.30.3),

BiocNeighbors (>= 1.14.0),

S4Vectors (>= 0.34.0),

BiocGenerics (>= 0.42.0),

Biostrings (>= 2.64.0),

BSgenome (>= 1.64.0),

GenomeInfoDb (>= 1.32.2),

IRanges (>= 2.30.0),

GenomicRanges (>= 1.48.0),

Rsamtools (>= 2.12.0),

GenomicAlignments (>= 1.32.1),

rtracklayer (>= 1.56.1),

GenomicFeatures (>= 1.48.3),

SummarizedExperiment (>= 1.26.1),

DEXSeq (>= 1.42.0),

igraph (>= 1.3.4),

scuttle (>= 1.6.2),

scran (>= 1.24.0),

fastmatch (>= 1.1-3),

pheatmap (>= 1.0.12),

ggbio (>= 1.44.1),

ggplot2 (>= 3.3.6),

biovizBase (>= 1.44.0)

License: GPL (>= 3)

URL: https://github.com/Genentech/Isosceles

Encoding: UTF-8

Roxygen: list(markdown = TRUE)

RoxygenNote: 7.2.1

Suggests:

testthat (>= 3.0.0),

tools (>= 4.2.0),

knitr (>= 1.39),

rmarkdown (>= 2.14),

BiocStyle (>= 2.24.0),

viridis (>= 0.6.2),

RColorBrewer (>= 1.1-3),

dittoSeq (>= 1.8.1),

Nebulosa (>= 1.0.1),

Seurat (>= 4.1.1),

scater (>= 1.24.0),

bluster (>= 1.6.0)

Config/testthat/edition: 3

LinkingTo:

Rcpp (>= 1.0.9),

RcppArmadillo (>= 0.11.2.0.0)

VignetteBuilder: knitr