# Generated by roxygen2: do not edit by hand

export(Kontextual)
export(calcContamination)
export(calcStateChanges)
export(getAbundances)
export(getDistances)
export(getMarkerMeans)
export(getParentPhylo)
export(isKontextual)
export(kontextCurve)
export(kontextPlot)
export(kontextualTest)
export(makeWindow)
export(parentCombinations)
export(plotStateChanges)
export(prepMatrix)
export(relabel)
export(relabelKontextual)
import(dplyr)
import(spatstat.geom)
import(tidyr)
importFrom(BiocParallel,
  MulticoreParam,
  SerialParam,
  SnowParam,
  bplapply,
  bpmapply,
  bpparam
)
importFrom(Rcpp,sourceCpp)
importFrom(SingleCellExperiment,
  "reducedDim<-",
  reducedDim,
  reducedDimNames
)
importFrom(SpatialExperiment,
  spatialCoords,
  spatialCoordsNames
)
importFrom(SummarizedExperiment,
  "colData<-",
  assay,
  assayNames,
  colData
)
importFrom(data.table,
  ":=",
  .SD,
  as.data.table,
  dcast
)
importFrom(dplyr,
  across,
  all_of,
  arrange,
  bind_rows,
  contains,
  filter,
  full_join,
  group_by,
  inner_join,
  left_join,
  mutate,
  relocate,
  rename,
  rename_with,
  select,
  slice,
  starts_with,
  summarise,
  summarise_at,
  vars
)
importFrom(edgeR,
  DGEList,
  glmQLFTest,
  glmQLFit,
  topTags
)
importFrom(ggplot2,
  aes,
  aes_string,
  autoplot,
  facet_wrap,
  geom_hline,
  geom_line,
  geom_point,
  geom_ribbon,
  geom_smooth,
  ggplot,
  ggtitle,
  guides,
  labs,
  scale_colour_gradientn,
  scale_fill_distiller,
  stat_density_2d,
  theme_classic,
  xlab,
  ylab
)
importFrom(limma,lmFit)
importFrom(methods,is)
importFrom(ranger,ranger)
importFrom(spatstat.geom,
  closepairs,
  owin,
  ppp
)
importFrom(stats,
  runif,
  sd
)
importFrom(stringr,
  str_detect,
  str_replace
)
importFrom(tibble,
  column_to_rownames,
  remove_rownames,
  rownames_to_column
)
importFrom(tidyr,
  gather,
  pivot_longer,
  pivot_wider
)
useDynLib(Statial, .registration = TRUE)
