https://github.com/jackhump/ftld-tdp_analysis
"All code written for Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions"
https://github.com/jackhump/ftld-tdp_analysis
Last synced: 5 months ago
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"All code written for Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions"
- Host: GitHub
- URL: https://github.com/jackhump/ftld-tdp_analysis
- Owner: jackhump
- Created: 2021-09-29T18:25:28.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2021-12-16T01:49:11.000Z (over 4 years ago)
- Last Synced: 2023-07-31T21:25:26.968Z (almost 3 years ago)
- Language: HTML
- Size: 19.1 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
## FTLD-TDP differential expression
Rahat Hasan 2021
All Rmarkdown workbooks written for the project.
Most workbooks are presented as raw .Rmd (in `scripts/` and knitted HTML files (in `html/`).
## Differential gene expression analysis
[Covariate selection and PCA](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_pca.html)
[FTLD-TDP vs control results](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_expression.html)
[C9orf72 & non-C9orf72 vs control results](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_expression_c9.html)
[Postmortem interval results](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_expression_pmi.html)
## Cellular profiling of DEGs
[Gene-set enrichment analysis (GSEA)](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_gsea.html)
[Expression-weighted cell-type enrichment (EWCE)](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_ewce.html)
[VEN and MMP gene expression](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_vens_and_mmps.html)
[Building sets of marker genes from Mathys et al](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/scripts/FTLD_deconvolution_pipeline.rmd)
[Cell-type deconvolution](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_deconvolution_results.html)
## Differential transcript usage analysis
[DTU results & overlaps with TDP-43 knockdown genes](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_transcript_usage.html)
[Enrichment results using DTU genes](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_transcript_usage_gsea.html)
## Correlations with deconvolution estimates
[All atrophy correlations](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_atrophy_correlations.html)
[Microglial burden correlations](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_microglia_correlations.html)
[DNA methylation correlations](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_dna_methylation.html)