KaryoTap Publication Codebook

Codebook for analyses in Mays et al., 2023

Data Availability

• The current stable version of the karyotapR package is available on CRAN.
• The development version and source code of karyotapR is available on Github.
• Documentation and analysis tutorials for karyotapR are available at https://joeymays.xyz/karyotapR.
• The source code for karyotapR version 0.1 used for this study is archived on Zenodo under DOI https://doi.org/10.5281/zenodo.8305561.
• Raw sequencing data and aligned reads are available at SRA under NCBI BioProject accession PRJNA950110.
• Tapestri Pipeline output data used in this study is availble at Zenodo under DOI https://doi.org/10.5281/zenodo.8305841.

Analysis

R Dependencies

Analysis:

• karyotapR v0.1
• here
• tidyverse
• GenomicRanges
• furrr
• emmeans
• scuttle

Plotting:

• ggplotify
• cowplot
• ggplot2
• ggrastr
• ComplexHeatmap
• karyoploteR
• ggdist
• geomtextpath

Scripts

# Experiment Files
rmarkdown::render('analysis-notebooks/exp01-karyotapr-analysis.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/exp04-karyotapr-analysis.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/exp05-karyotapr-analysis.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure 1
rmarkdown::render('analysis-notebooks/Figure-A_panel-maps.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-01.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure S1
rmarkdown::render('analysis-notebooks/Figure-B_heatmap-clustering.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-S01.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure 2
rmarkdown::render('analysis-notebooks/Figure-C-sensitivity-specificity.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-02.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure 3
rmarkdown::render('analysis-notebooks/Figure-03.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure S2
rmarkdown::render('analysis-notebooks/Figure-S02.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure 4
##hpc
##rmarkdown::render('analysis-notebooks/Figure-D-downsample-sim.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-D-downsample-analysis.Rmd', 'html_notebook', output_dir = "analysis-html"
##hpc
##rmarkdown::render('analysis-notebooks/Figure-E-panel-sim.Rmd', 'html_notebook', output_dir = "analysis-html"
##rmarkdown::render('analysis-notebooks/Figure-E-panel-sim-3component.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-E-panel-analysis.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-E-panel-analysis-3component.Rmd', 'html_notebook', output_dir = "analysis-html"
##hpc
##rmarkdown::render('analysis-notebooks/Figure-G-depth-sim.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-G-depth-analysis.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-04.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure S3
rmarkdown::render('analysis-notebooks/Figure-S03.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure 5 
#need 3 component
rmarkdown::render('analysis-notebooks/Figure-I_exp4_sensitivity.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-J_exp4_barcoding.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-05.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure 6
rmarkdown::render('analysis-notebooks/Figure-K_exp5_karyocreate.Rmd', 'html_notebook', output_dir = "analysis-html"
rmarkdown::render('analysis-notebooks/Figure-06.Rmd', 'html_notebook', output_dir = "analysis-html"

# Figure S4
rmarkdown::render('analysis-notebooks/Figure-S04.Rmd', 'html_notebook', output_dir = "analysis-html"