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Last updated: 2022-03-24

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Knit directory: cacoaAnalysis/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

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Repository version: 549d728

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	549d728	viktor_petukhov	2022-03-24	Updated index.Rmd
html	f04119a	viktor_petukhov	2022-01-14	Recompiled index.html
Rmd	87ff580	viktor_petukhov	2022-01-14	Updated index.Rmd
html	936872f	Viktor Petukhov	2021-12-16	Recompiled index
Rmd	fc9433f	Viktor Petukhov	2021-12-16	Updated index
html	94eff35	viktor_petukhov	2021-12-12	Compiled all individual reports
html	80cd443	viktor_petukhov	2021-12-10	Updated functions; rebuilt index
Rmd	27eea48	viktor_petukhov	2021-12-09	Updated individual dataset reports
html	b587974	viktor_petukhov	2021-12-08	Compiled AZ report
Rmd	cafbfd6	viktor_petukhov	2021-12-08	AZ report
Rmd	c7b1293	viktor_petukhov	2021-12-08	ASD report
Rmd	8d0aaaf	viktor_petukhov	2021-12-08	Epilepsy report
Rmd	91efca9	viktor_petukhov	2021-12-08	MS report
html	55cdc41	viktor_petukhov	2021-12-06	Compiled notebooks
Rmd	20c18c5	viktor_petukhov	2021-12-06	Distance simulation notebook
html	697edea	viktor_petukhov	2021-11-30	Build structure notebooks
Rmd	269c679	viktor_petukhov	2021-11-30	Structure Rmds
Rmd	5e70bd6	viktor_petukhov	2021-11-23	Start workflowr project.

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Table of content

Figures

• F2: Compositional data analysis, cluster-based
• F3: Compositional data analysis, cluster-free
• F4, S1,2: Expression changes (cluster-based) and sample heterogeneity
  • F4 and S1: Expression change magnitudes, cluster-based
  • F4 and S2: Analysis of sample heterogeneity
• F5 and S3: Differential Expression analysis
  • DE stability
  • Improving DE stability with the Genetic Algorithm
  • DE and GSEA biological analysis
• F6 and S4: Gene expression analysis, cluster-free
• F7: Functional interpretation

Preprocessing

• Dataset preprocessing
• Cacoa preprocessing

Simulations

• Simulations for different cell types (also generates the necessary data)
• Simulations for num. of cells and num. of samples
• Simulation for sensitivity to DE fraction change
• Simulation for sensitivity to log2-fold change
• Different normalization types

Individual dataset reports

• Alzheimer
• Autism
• Epilepsy
• Multiple Sclerosis
• Pulmonary Fibrosis
• Squamous Cell Carcinoma

Data preparation

To download the raw data, you need to run Rscript ./code/download_data.R from the project folder. After that, you need to run two scripts from the ‘Preprocessing’ section: first dataset preprocessing and then Cacoa preprocessing.