Tools for RNAseq Analyses

This is basically a list of resources that I have put together as a reference for my own research, but I'm publishing it here in case it might help others

Methods

• [Review papers]({{ site.baseurl }}/Methods/Reviews)
• [De Novo Transcriptome Assembly]({{ site.baseurl }}/Methods/DeNovo)
• [Alignment Tools]({{ site.baseurl }}/Methods/Alignment)
• [Reference-Based Transcript Identification]({{ site.baseurl }}/Methods/TranscriptDiscovery)
• [Quantification Tools]({{ site.baseurl }}/Methods/Quantification)
• [Normalization Methods]({{ site.baseurl }}/Methods/Normalization)
• [Batch Correction]({{ site.baseurl }}/Methods/BatchCorrection)
• [Differential Expression]({{ site.baseurl }}/Methods/DE)
• [Differential Splicing]({{ site.baseurl }}/Methods/Splicing)
• [eQTL Analyses]({{ site.baseurl }}/Methods/eQTL)
• [Gene-trait Association]({{ site.baseurl }}/Methods/GeneTraitAssociation)
• [Pathway Analyses]({{ site.baseurl }}/Methods/Pathways)

Other Resources

• [GTEx Publications]({{ site.baseurl }}/Resources/GTExPapers)
• [Brain Gene Expression Resources]({{ site.baseurl }}/Resources/BrainExpression)

Workflow Tutorials

• [System Configuration]({{ site.baseurl }}/WorkflowTutorial/SystemConfig)
• [Version Control]({{ site.baseurl }}/WorkflowTutorial/GitIntro)
• [Snakemake]({{ site.baseurl }}/WorkflowTutorial/SnakeMake)
• [Tidy R]({{ site.baseurl }}/WorkflowTutorial/TidyR)
• [Databases]({{ site.baseurl }}/WorkflowTutorial/Databases)
• [Shiny]({{ site.baseurl }}/WorkflowTutorial/Shiny)