Matrix data file is used for heat map drawing, which can filter, normalize and cluster matrix data. It is mostly used for cluster analysis of gene expression level between different samples.
Gene function annotation is performed by mapping sequences in FASTA file against various database.
Basic Local Alignment Search Tool
This tool is designed to predict coding regions (CDS) and non-coding regions (UTR) in given transcript sequences based on blasting against known protein database and ORF prediction.
Manhattan plot enables display of data with a large number of data points. It is commonly used in genome-wide association studies (GWAS).
CIRCOS diagram enables direct presentation of SNP, InDeL, SV, CNV distributions on genome.
TopGO is a tool designed for functional enrichment. TopGO-Bioconductor package consists differential expression analysis, GO enrichment analysis and visualization of the results. It will generate a folder with output named "Graph", which contains results for topGO_BP, topGO_CC and topGO_MF.
WGCNA is a widely used data mining method for discovering gene co-expression modules. It is applicable to various expression dataset including microarray data and gene expression data originated from next generation sequencing.
InterPro protein sequence analysis and classification
This tool is design to generate GO enrichment histogram, KEGG enrichment histogram and KEGG enrichment pathway based on provided gene set and corresponding annotation.