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DESCRIPTION
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DESCRIPTION
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Package: malacoda
Title: Bayesian Analysis of High-Throughput Genomic Assays
Version: 0.2.2
Authors@R: c(
person(given = "Andrew",
family = "Ghazi",
role = c("aut", "cre"),
email = "arghazi@bcm.edu"),
person("Trustees of", "Columbia University",
role = "cph",
comment = "R/stanmodels.R and tools/make_cc.R"))
Description: Bayesian analysis of high-throughput genomic assays, such as Massively
Parallel Reporter Assays (MPRA) and clustered regularly interspaced short
palindromic repeat (CRISPR) screens. The output counts, whether MPRA barcodes
or CRISPR gRNAs, are modelled as coming from a negative binomial distribution
with empirical gamma priors. The empirical priors can be refined through the
use of user-input annotations, further improving model performance.
License: GPL (>=3)
Depends:
methods,
R (>= 3.5.0),
Rcpp (>= 0.12.18)
Imports:
rstan (>= 2.17.3),
rstantools (>= 1.5.1),
dplyr,
purrr,
magrittr,
tidyr,
stringr,
parallel,
stats,
coda,
mvtnorm,
broom,
ggbeeswarm,
rlang,
ggplot2,
tibble,
readr
LinkingTo:
BH (>= 1.66.0-1),
Rcpp (>= 0.12.18),
RcppEigen (>= 0.3.3.4.0),
rstan (>= 2.17.3),
StanHeaders (>= 2.17.2)
URL: https://github.com/andrewGhazi/malacoda
BugReports: https://github.com/andrewGhazi/malacoda/issues
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
SystemRequirements: GNU make, FASTX-Toolkit, sed, FreeBarcodes
RoxygenNote: 7.0.2
Suggests: knitr,
rmarkdown,
kdensity,
gridExtra
VignetteBuilder: knitr