├── .gitignore ├── GRCh38.p13_annotation.csv ├── README.md ├── align_STAR.py ├── bulk-rnaseq-analysis-guide.Rmd ├── combine_STAR_output.py ├── docs └── index.html ├── fastq_download.py ├── h.all.v7.0.symbols.gmt.txt ├── images └── figure-gfm │ ├── default-plot-counts-baseR-1.png │ ├── default-plot-counts-ggplot2-1.png │ ├── differential-gene-heatmap-1.png │ ├── distance-plot-1.png │ ├── gsea-enrichment-plot-1.png │ ├── gsea-enrichment-plot-2.png │ ├── gsea-waterfall-plot-1.png │ ├── logfoldchange-comparison-plot-1.png │ ├── pca-plot-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-20-2.png │ ├── upgraded-plot-counts-1.png │ ├── variable-gene-heatmap-all-samples-1.png │ ├── variable-gene-heatmap-separate-samples-1.png │ └── volcano-plot-1.png ├── output ├── LNCAP_Hypoxia_vs_LNCAP_Normoxia_allgenes.csv ├── LNCAP_Hypoxia_vs_LNCAP_Normoxia_cpm_cutoff.csv ├── LNCAP_Hypoxia_vs_LNCAP_Normoxia_log2f_cutoff.csv ├── LNCAP_Hypoxia_vs_LNCAP_Normoxia_padj_cutoff.csv ├── LNCAP_Hypoxia_vs_LNCAP_Normoxia_rank.rnk ├── PC3_Hypoxia_vs_PC3_Normoxia_allgenes.csv ├── PC3_Hypoxia_vs_PC3_Normoxia_cpm_cutoff.csv ├── PC3_Hypoxia_vs_PC3_Normoxia_log2f_cutoff.csv ├── PC3_Hypoxia_vs_PC3_Normoxia_padj_cutoff.csv ├── PC3_Hypoxia_vs_PC3_Normoxia_rank.rnk └── gene_annotated_normalized_counts.csv ├── qc.csv └── raw_counts.csv /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/erilu/bulk-rnaseq-analysis/HEAD/.gitignore -------------------------------------------------------------------------------- /GRCh38.p13_annotation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/erilu/bulk-rnaseq-analysis/HEAD/GRCh38.p13_annotation.csv -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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