Next Generation Sequence (NSG) Analysis
  • Bowtie : Bowtie is an ultrafast, memory-efficient short read aligner

  • TopHat : A spliced read mapper for RNA-Seq

  • Cufflinks : Transcript assembly, differential expression, and differential regulation for RNA-Seq


Microarray Analysis
  • ArrayMiner : Set of analysis tools using advanced algorithms to reveal the true structure of gene expression data.

  • HeatMap Builder : Generates customizable heatmaps from microarray data

  • GeneX : Gene Expression Database : integrated toolset for data analysis and comparison


SNP Anlaysis
  • SNPMiner : A SNP database and web interface with the functionalities including search, candidate SNP selections, and genetic analysis.

  • SeattleSNPs : Provides access to more than 125 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.

  • SNPper: Retrieve known SNPs by position or by association with a gene.

  • Haploview : Visualization of SNP location in a genomic region.


Pathway Analysis
  • WebGestalt : a WEB-based gene set Analysis Toolkit.

  • IPA : Identifies relationships, mechanisms, functions, and pathways of relevance in data. It also has resources to easily search scientific literature for genes or pathways of interest.

  • Cytoscape : Pathway / graph visualization


GWAS Analysis
  • dmGWAS : an R package for genome-wide association studies (GWAS) analysis.

  • PLINK : Genome association analysis toolset.


R Packages
  • Affy : Methods for Affymetrix Oligonucleotide Arrays.

  • Limma : Linear Models for Microarray Data.

  • Ringo : R Investigation of ChIP-chip Oligoarrays.

  • DESeq : Calculates the gene expression differences based on read counts.