rmyknife

• 💾 Installation
• 🧠 Memoise for BiomaRt
• ♻️ Using Ensembl mirror
• ⏳ History

The goal of rmyknife is to provide a centralized place for R functions that I often use but that do not belong to a more specialized package yet. This package will probably be pretty messy.

💾 Installation

You can install the github version of rmyknife with:

library(devtools)
devtools::install_github("paulklemm/rmyknife")

🧠 Memoise for BiomaRt

For interfacing Biomart, we are using the memoise package. It will store all queries to a folder names rmyknife_memoise in your r temp folder. You can set the following options to customize this behavior.

options(rmyknife.use_memoise = FALSE)
options(rmyknife.memoise_path = "<some/other/path>")

♻️ Using Ensembl mirror

Sometimes the Ensembl biomart server are unstable. To still be able to conduct queries, we support alternative hosts which can be set as follows.

# rmyknife.use_biomart_mirror = TRUE will use "useast.ensembl.org" as default
# You can specify a custom mirror using rmyknife.biomart_mirror_host
options(
  rmyknife.verbose = TRUE,
  rmyknife.use_biomart_mirror = TRUE,
  rmyknife.biomart_mirror_host = "useast.ensembl.org"
  # rmyknife.biomart_mirror_host = "uswest.ensembl.org"
  # rmyknife.biomart_mirror_host = "asia.ensembl.org"
)

⏳ History

• 2023-08-04
  • Add workers to make
  • Bump to 0.2.9
• 2022-10-07
  • Enhance make
  • Bump to 0.2.8
• 2022-10-06
  • Add make for making and loading targets
  • Bump to 0.2.7
• 2022-09-28
  • Add get_gzipped_stream, get_uniprot and get_uniprot_with_ensembl
  • Bump to 0.2.6
• 2022-08-15
  • Add highlight parameter to plot_volcano. Bump to 0.2.5
• 2022-07-22
  • Add plot_volcano. Bump to 0.2.4
• 2021-09-06
  • Add rnorvegicus to get_ensembl_dataset_from_version. Bump to 0.2.3
• 2021-04-19
  • Add set_ggplot_defaults. Bump to 0.2.2
• 2021-02-22
  • Add option to get children of GO-terms
  • Bump version to 0.2.1
• 2021-02-19
  • Get GO-name based on biomaRt, not GO.db
  • Allow custom biomart to be used in attach_biomart
  • Bump version to 0.2.0
• 2020-11-23
  • Fix rare attach_biomart bug
  • Bump version to 0.1.10
• 2020-10-26
  • Remove tidylog dependency
  • Bump version to 0.1.9
• 2020-08-05
  • Add print_params function
  • Bump version to 0.1.7
• 2020-08-04
  • Add get_tempfile_from_url
  • Bump version to 0.1.6
• 2020-07-27
  • Add attach_gene_symbol_from_entrez and ensembl_to_entrez from mygo package
  • Bump version to 0.1.5
• 2020-07-02
  • Fix minor deprecated calls to avoid warning messages from tibble and dplyr
  • Bump version to 0.1.4
• 2020-06-24
  • Add deseq2_result_to_tibble function for converting deseq2 result objects to a dataframe
  • Bump version to 0.1.3
• 2020-05-25
  • Add write_xls function
  • Add options options(rmyknife.use_biomart_mirror = TRUE), options(rmyknife.biomart_mirror_host = "useast.ensembl.org") and options(rmyknife.verbose = TRUE)
  • Bump version to 0.1.2
  • Close Remove hack while Ensembl is being transferred #1
• 2020-04-29
  • Add dt_datatable function
  • Bump version to 0.1.0
• 2020-04-22
  • Add function get_gene_counts_per_cell
  • Bump version to 0.0.5
• 2020-03-21
  • Add Remove hack while Ensembl is being transferred #1
  • Bump version to 0.0.4
• 2020-02-04
  • Added get_genes_of_goterm_godb function
• 2019-11-14
  • Added get_seurat_clustering function
• 2019-11-13
  • Added read_cellranger_feature_bc_matrix and read_cellranger_feature_bc_matrix_h5 function for reading 10x genomics cellranger data