Package: pictographPlus
Type: Package
Title: Reconstructing Clone-Resolved Transcriptional Programs from Bulk Tumor Sequencing
Version: 1.1.1
Authors@R: c(
    person("Jiaying", "Lai", email = "jlai33@jh.edu", role = c("aut", "cre")),
    person("Yi", "Yang", role = "aut"),
    person("Rachel", "Karchin", email = "karchin@jhu.edu", role = c("aut", "ths")))
Description: Integrates bulk DNA and RNA sequencing data to reconstruct
    clone-specific transcriptomic profiles, infer tumor clonal evolution, and
    identify functional transitions between clones. Tumor evolution is inferred
    from single- or multi-region sequencing by modeling the uncertainty of
    mutation cellular fraction in small somatic mutations and copy number
    alterations using a Bayesian hierarchical model. Bulk gene expression is
    then deconvolved by integrating clone tree structure with clone proportions
    across samples, optimizing an objective that balances reconstruction error
    against a tree-aware smoothness penalty so closely related clones display
    similar expression. Pathway enrichment analysis identifies statistically
    significant alterations in pathways connecting tumor clones.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports:
  readr (>= 2.1.4),
  dplyr (>= 1.1.1),
  tidyr (>= 1.3.0),
  tibble (>= 3.2.0),
  purrr (>= 1.0.2),
  stringr (>= 1.5.0),
  ggplot2 (>= 3.4.0),
  magrittr (>= 2.0.3),
  methods,
  parallel,
  rjags (>= 4-16),
  epiR (>= 2.0.0),
  LaplacesDemon (>= 16.1.6),
  igraph (>= 2.0.1),
  viridis (>= 0.6.5),
  ggmcmc (>= 1.5.1),
  UpSetR (>= 1.4.0),
  cluster (>= 2.1.4),
  fgsea (>= 1.28.0),
  ggrepel (>= 0.9.6),
  diptest (>= 0.77-1),
  pheatmap (>= 1.0.12),
  DESeq2 (>= 1.42.0),
  GenomicRanges (>= 1.54.0),
  IRanges (>= 2.36.0)
Suggests:
  knitr,
  rmarkdown,
  testthat (>= 3.0.0)
VignetteBuilder: knitr
RoxygenNote: 7.3.2
URL: https://github.com/KarchinLab/pictographPlus
BugReports: https://github.com/KarchinLab/pictographPlus/issues
