data-raw/downrefs.R

In rnabioco/clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

library(tidyverse)

d1 <- c(
  paste0(
    "[",
    "ref_MCA",
    "](",
    "https://github.com/rnabioco/clustifyrdata/raw/master/data/ref_MCA.rda",
    ")"
  ),
  "Mouse Cell Atlas",
  dim(clustifyrdata::ref_MCA)[2],
  dim(clustifyrdata::ref_MCA)[1],
  "mouse",
  paste0(
    "[from](",
    "https://www.cell.com/cell/fulltext/S0092-8674(18)30116-8",
    ")"
  )
)

d2 <- c(
  paste0(
    "[",
    "ref_tabula_muris_drop",
    "](",
    "https://github.com/rnabioco/clustifyrdata/raw/master/data/ref_tabula_muris_drop.rda",
    ")"
  ),
  "Tabula Muris (10X)",
  dim(clustifyrdata::ref_tabula_muris_drop)[2],
  dim(clustifyrdata::ref_tabula_muris_drop)[1],
  "mouse",
  paste0("[from](", "https://www.nature.com/articles/s41586-018-0590-4", ")")
)

d3 <- c(
  paste0(
    "[",
    "ref_tabula_muris_facs",
    "](",
    "https://github.com/rnabioco/clustifyrdata/raw/master/data/ref_tabula_muris_facs.rda",
    ")"
  ),
  "Tabula Muris (SmartSeq2)",
  dim(clustifyrdata::ref_tabula_muris_facs)[2],
  dim(clustifyrdata::ref_tabula_muris_facs)[1],
  "mouse",
  paste0("[from](", "https://www.nature.com/articles/s41586-018-0590-4", ")")
)

d4 <- c(
  paste0(
    "[",
    "ref_mouse.rnaseq",
    "](",
    "https://github.com/rnabioco/clustifyrdata/raw/master/data/ref_mouse.rnaseq.rda",
    ")"
  ),
  "Mouse RNA-seq from 28 cell types",
  dim(clustifyrdata::ref_mouse.rnaseq)[2],
  dim(clustifyrdata::ref_mouse.rnaseq)[1],
  "mouse",
  paste0(
    "[from](",
    "https://genome.cshlp.org/content/early/2019/03/11/gr.240093.118",
    ")"
  )
)

d5 <- c(
  paste0(
    "[",
    "ref_moca_main",
    "](",
    "https://github.com/rnabioco/clustifyrdata/raw/master/data/ref_moca_main.rda",
    ")"
  ),
  "Mouse Organogenesis Cell Atlas (main cell types)",
  dim(clustifyrdata::ref_moca_main)[2],
  dim(clustifyrdata::ref_moca_main)[1],
  "mouse",
  paste0("[from](", "https://www.nature.com/articles/s41586-019-0969-x", ")")
)

d6 <- c(
  paste0(
    "[",
    "ref_hema_microarray",
    "](",
    "https://github.com/rnabioco/clustifyrdata/raw/master/data/ref_hema_microarray.rda",
    ")"
  ),
  "Human hematopoietic cell microarray",
  dim(clustifyrdata::ref_hema_microarray)[2],
  dim(clustifyrdata::ref_hema_microarray)[1],
  "human",
  paste0("[from](", "https://www.cell.com/fulltext/S0092-8674(11)00005-5", ")")
)

d7 <- c(
  paste0(
    "[",
    "ref_cortex_dev",
    "](",
    "https://github.com/rnabioco/clustifyrdata/raw/master/data/ref_cortex_dev.rda",
    ")"
  ),
  "Human cortex development scRNA-seq",
  dim(clustifyrdata::ref_cortex_dev)[2],
  dim(clustifyrdata::ref_cortex_dev)[1],
  "human",
  paste0(
    "[from](",
    "https://science.sciencemag.org/content/358/6368/1318.long",
    ")"
  )
)

d8 <- c(
  paste0(
    "[",
    "ref_pan_indrop",
    "](",
    "https://github.com/rnabioco/clustifyrdata/raw/master/data/ref_pan_indrop.rda",
    ")"
  ),
  "Human pancreatic cell scRNA-seq (inDrop)",
  dim(clustifyrdata::ref_pan_indrop)[2],
  dim(clustifyrdata::ref_pan_indrop)[1],
  "human",
  paste0("[from](", "https://www.cell.com/fulltext/S2405-4712(16)30266-6", ")")
)

d9 <- c(
  paste0(
    "[",
    "ref_pan_smartseq2",
    "](",
    "https://github.com/rnabioco/clustifyrdata/raw/master/data/ref_pan_smartseq2.rda",
    ")"
  ),
  "Human pancreatic cell scRNA-seq (SmartSeq2)",
  dim(clustifyrdata::ref_pan_smartseq2)[2],
  dim(clustifyrdata::ref_pan_smartseq2)[1],
  "human",
  paste0(
    "[from](",
    "https://www.sciencedirect.com/science/article/pii/S1550413116304363",
    ")"
  )
)

d <- data.frame(d1, d2, d3, d4, d5, d6, d7, d8, d9) %>% t()
colnames(d) <- c("name", "desc", "ntypes", "ngenes", "org", "from_pub")
downrefs <- d %>% as.tibble()
usethis::use_data(downrefs, compress = "xz", overwrite = TRUE)