rexseek

Overview

R package for matrix processing in the exSeek project

Install

Some functions only works in Bioconductor 3.7

For Students in Lu Lab, this step is not needed (and even causes error) if you run R on cnode.

if (!requireNamespace("BiocManager")) install.packages('BiocManager');
BiocManager::install(version = '3.7', ask = F, update = F)

Then you can install the package

if (!requireNamespace("remotes")) install.packages('remotes');
remotes::install_github('dongzhuoer/rexseek', upgrade = F);

Usage

For students in Lu Lab, please refer to this guide

The following parts are for package maintainers.

to do

document as_SingleCellExperiment()
error message follow style guide
add R-raw/data-raw.Rmd (move some Non-Git code in)

useful location

https://github.com/lulab/exSeek-dev/blob/master/docs/matrix_processing.md http://166.111.156.58:8000/jupyter/user/zhuoer/notebooks/exseek/jupyter/matrix_processing.ipynb

develop

Refer to this post

Non-Git

files neccessary for developing the packages

'data-raw/external/all.txt' %>% readr::read_tsv() %>% 
	dplyr::select('transcript_id', gene_type = 'transcript_type') %>%
    readr::write_rds('data-raw/rna_type.rds', 'xz')

files used in real-case testing

data-raw/external/ can be found in dongzhuoer/lulab-rotation-summary repo, exseek/ folder

Credits

rna_type comes from Binbin Shi

xyfzkd / rexseek