README.md

In bhagwataditya/importomics: Unified statistal Modeling of Omics Data

title: autonomics subtitle: generifying and intuifying cross-platform omics analysis

# Install
    install.packages('remotes')
    remotes::install_github('bhagwataditya/autonomics',  
                             repos = BiocManager::repositories(), 
                             dependencies = TRUE, upgrade = FALSE)

# Run
    file <- download_data('billing16.bam.zip')                     # RNAseq BAM
    read_rnaseq_bams(file, paired=TRUE, genome = 'hg38')

    file <- download_data('billing16.rnacounts.txt')               # RNAseq counts
    read_rnaseq_counts(file)

    file <- download_data('halama18.metabolon.xlsx')               # Metabolon xlsx
    read_metabolon(file)

    select <- sprintf('%s_STD', c('E00', 'E01', 'E02', 'E05', 'E15', 'E30', 'M00'))
    proteingroups <- download_data('billing19.proteingroups.txt')  # LCMSMS Proteingroups
    read_proteingroups(proteingroups, select_subgroups = select)

    phosphosites <- download_data('billing19.phosphosites.txt')    # LCMSMS Phosphosites
    read_phosphosites(phosphosites, proteingroups, select = select_subgroups)

    file <- download_data('atkin18.somascan.adat')                 # SOMAscan adat
    read_somascan(file)

bhagwataditya/importomics documentation built on April 15, 2024, 4:12 p.m.