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Recommended Reading

  • Recommended Coverage and Read Depth
  • Illumina Coverage Calculator
  • RNA-seq data analysis: Best Practices
  • Aligner Comparison
  • Guide to Analysis of RNA-seq Data
  • Alignment Visualization software
  • SeqAnswers
  • Mothur (Microbial ecology)
  • NEB rRNA Depletion
  • Ribo-off rRNA Depletion (bacteria)
  • riboPOOL
  • Ribo Minus
  • Gene Fusion Detection
  • Alignment algorithms

DNA Analysis

  • Franklin (variant classification)
  • AmpliCancer - variant discovery tool
  • SNPnexus
  • Genome Analysis Tool Kit (GATK)
  • Gemini (variant annotation)
  • VarAFT
  • Mutation Taster

miRNA Analysis

  • miRWalk 2.0
  • miRMaster 2.0
  • mirBase
  • TargetScan
  • Qiagen GeneGlobe
  • Tissue Atlas

circRNA Analysis

  • circBase
  • Circular RNA Interactome

ChIP-seq Analysis

  • ChIP-seq Peak Annotation and Functional Analysis

Single Cell Resources

  • 10x Genomics Publications resource
  • 10x Genomics Analysis guides
  • How many cells
  • Cite-seq
  • SEURAT
  • Tutorial: guidelines for annotating single-cell transcriptomic maps

Enrichment Analysis

  • Enrichr
  • Reactome
  • g:Profiler
  • Metascape
  • GSEA
  • DAVID
  • Panther
  • GOrilla

Network Analysis

  • String
  • Cytoscape
  • Interferome
  • GeneMania

Biological Interpretation

  • AltAnalyze
  • CiiiDER
  • The Bio-Analytic Resource for Plant Biology

Other NGS Tools

  • FastQC
  • PRINSEQ
  • Galaxy
  • IGV
  • R Power Analysis
  • Venny 2.1

qPCR Resources

  • qPCR Handbook

About Us

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  • Contact Us

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