# Gene-level RNA-Seq Data Analysis (lagacy)

## Gene-level RNA-Seq Data Analysis (lagacy)

- [Introduction](https://ycl6.gitbook.io/rna-seq-data-analysis/master.md)
- [RNA-Seq Analysis Workflow](https://ycl6.gitbook.io/rna-seq-data-analysis/rna-seq_analysis_workflow.md)
- [Login to server](https://ycl6.gitbook.io/rna-seq-data-analysis/rna-seq_analysis_workflow/login_to_server.md)
- [Obtain data and software](https://ycl6.gitbook.io/rna-seq-data-analysis/rna-seq_analysis_workflow/obtain_data.md)
- [Create mapping indices](https://ycl6.gitbook.io/rna-seq-data-analysis/rna-seq_analysis_workflow/create_mapping_indices.md)
- [Mapping with STAR](https://ycl6.gitbook.io/rna-seq-data-analysis/rna-seq_analysis_workflow/mapping_with_star.md)
- [Quantification using RSEM](https://ycl6.gitbook.io/rna-seq-data-analysis/rna-seq_analysis_workflow/quantification_using_rsem1.md)
- [De novo assembly using Trinity](https://ycl6.gitbook.io/rna-seq-data-analysis/de_novo_assembly_using_trinity.md)
- [De novo assembly of RNA-Seq reads](https://ycl6.gitbook.io/rna-seq-data-analysis/de_novo_assembly_using_trinity/de_novo_assembly_of_rna-seq_reads.md)
- [Compare de novo reconstructed transcripts to reference annotations](https://ycl6.gitbook.io/rna-seq-data-analysis/de_novo_assembly_using_trinity/compare_de_novo_reconstructed_transcripts_to_reference_annotations.md)
- [Quantification using RSEM](https://ycl6.gitbook.io/rna-seq-data-analysis/de_novo_assembly_using_trinity/quantification_using_rsem2.md)
- [Differential expression analysis using R](https://ycl6.gitbook.io/rna-seq-data-analysis/differential_expression_analysis_using_r.md)
- [Install R libraries](https://ycl6.gitbook.io/rna-seq-data-analysis/differential_expression_analysis_using_r/install_r_libraries.md)
- [Perform DE analysis](https://ycl6.gitbook.io/rna-seq-data-analysis/differential_expression_analysis_using_r/perform_de_analysis.md)
- [Perform DE analysis (Trinity)](https://ycl6.gitbook.io/rna-seq-data-analysis/differential_expression_analysis_using_r/perform_de_analysis_trinity.md)
- [Extracting DE transcripts and generating heatmaps (Trinity)](https://ycl6.gitbook.io/rna-seq-data-analysis/differential_expression_analysis_using_r/extracting_de_transcripts_and_generating_heatmaps_trinity.md)
- [Visualization](https://ycl6.gitbook.io/rna-seq-data-analysis/visualization.md)