{"id":39555313,"url":"https://github.com/jackhump/ftld-tdp_analysis","last_synced_at":"2026-01-18T07:01:04.211Z","repository":{"id":185141749,"uuid":"411786603","full_name":"jackhump/FTLD-TDP_analysis","owner":"jackhump","description":"\"All code written for Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain 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FTLD-TDP differential expression\n\nRahat Hasan 2021\n\nAll Rmarkdown workbooks written for the project.\n\nMost workbooks are presented as raw .Rmd (in `scripts/` and knitted HTML files (in `html/`).\n\n## Differential gene expression analysis\n[Covariate selection and PCA](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_pca.html)\n\n[FTLD-TDP vs control results](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_expression.html)\n\n[C9orf72 \u0026 non-C9orf72 vs control results](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_expression_c9.html)\n\n[Postmortem interval results](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_expression_pmi.html)\n\n## Cellular profiling of DEGs\n[Gene-set enrichment analysis (GSEA)](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_gsea.html)\n\n[Expression-weighted cell-type enrichment (EWCE)](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_ewce.html)\n\n[VEN and MMP gene expression](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_vens_and_mmps.html)\n\n[Building sets of marker genes from Mathys et al](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/scripts/FTLD_deconvolution_pipeline.rmd)\n\n[Cell-type deconvolution](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_deconvolution_results.html)\n\n## Differential transcript usage analysis\n[DTU results \u0026 overlaps with TDP-43 knockdown genes](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_transcript_usage.html)\n\n[Enrichment results using DTU genes](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_differential_transcript_usage_gsea.html)\n\n## Correlations with deconvolution estimates\n[All atrophy correlations](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_atrophy_correlations.html)\n\n[Microglial burden correlations](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_microglia_correlations.html)\n\n[DNA methylation correlations](https://github.com/jackhump/FTLD-TDP_analysis/blob/main/html/FTLD_dna_methylation.html)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjackhump%2Fftld-tdp_analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjackhump%2Fftld-tdp_analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjackhump%2Fftld-tdp_analysis/lists"}