main_directory='/path/to/Projects/'
investigator='investigator'
project_title='{{Genesee.title}}'
authors = '{{Genesee.authors}}'
type = 'RNA'
# devtools::load_all("path/to/GeneseeBulk")
# devtools::load_all("path/to/Genesee")
## or
library(GeneseeBulk)
library(Genesee)
#### set up directories and create sample file
geneseesc_skeleton(main_directory, investigator, project_title, authors = authors, project_type = type)
rmarkdown::render('01_load.Rmd', params = list( input_tsv = "deSeq_counts.txt",
input_project = NULL,
sample_sheet_csv= "all_samples_file.csv",
output_root= "refined/01load"), output_dir = 'reports')
rmarkdown::render('02_qc_dea.Rmd',
params = list(input_root = 'refined/01load_se.rds',
se_subset = NULL,
design_csv = 'extradata/fe_design.csv',
sample_id = 'sample_id',
plot_covariates = c("group", "tp", "mouse_group"),
dea_method = 'deseq2',
cache = TRUE,
output_root = "refined/02_qc_dea"
), output_dir = 'reports',
output_file = '02_qc_dea.html'
)
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