oncomiRDB

A Database for Oncogenic & Tumor-Suppressive MicroRNAs

ASEB

A Web Server for KAT-specific Acetylation Site Prediction

FastDMA

An integrative and fast analyzer for Infinium HumanMethylation450 beadchip (450k methylation array) data

miRHiC

Enrichment analysis of miRNA targets (or any other regulators) in hierarchical gene co-expression signatures

NURD

NURD is a software to estimate isoform/gene expression level of the RNA-Seq sample. It takes the non-uniform distribution of RNA-Seq into consideration

DSGseq

DSGseq is aimed to identify differentially spliced genes from two groups of RNA-seq samples.

SeqSite

ChIP-Seq Binding Site Identification (SeqSite) was developed for detecting transcription factor binding sites from ChIP-seq data.

SeqSaw

Short Spliced Sequence Mapping (SeqSaw) is a package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

DEGseq

Differentially Expressed Genes from RNA-seq data (DEGseq) is an R package to identify differentially expressed genes from RNA-Seq data.

TAGS

TAGS is a tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations.

CURE

CURE (Cytidine-to-Uridine Recognizing Editor) is a computational tool which predicts C-to-U RNA editing sites using evolutionary information.

OSCAR

One-class SVM for Cis-elements Accurate Recognition is a program that can be used to identify binding sites of known transcription factors on promoter regions.

PhoScan

Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach.

SubMito

SubMito is the first computational system for predicting protein submitochondria locations from its primary sequence. SubMito is designed and implemented with Java. This site is a web-like front end for SubMito system.

PCS

A stand-alone pakage to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3′-UTRs.

MethCGI

MethCGI is a tool to predict the methylation status of CpG islands in the human brain, developed on the data from human brain DNA using support vector machine (SVM).

Triplet-SVM

This program is developed for predicting a query sequence with hairpin structure as a real miRNA precursor or not. The triplet-SVM classifier analyzes the triplet elements of the query and predicts it using a SVM classifier.

MirAlign

An online tool to identify homologous miRNA genes. This tool can search for new miRNA candidates by requiring structural similarity and sequence conservations between new candidates and experimentally identified miRNAs.

RNAseqViewer

RNAseqViewer let you visualize the various data from the RNA-Seq analyzing process, for single or multiple samples.

Cipher

Correlating protein interaction network and phenotype network to predict disease genes.

DGPsubNet

inferBind

inferBind is a C++package to infer the binding positions of drug-protein interactions

ulfasQTL

ulfasQTL is a R package to find splicing QTL.

Databases


ATIE

Alternative Translational Initiation Database(ATID) is established to provide data of publicly available genes, alternatively translational isoforms and their detailed annotation.

dbRES

dbRES is a web-oriented comprehensive database for RNA Editing Site. dbRES contain only experimental validated RNA Editing Site. All the data in dbRES was manually collected from literatures reporting related experiment result or the GeneBank database.

dbSUPER

dbSUPER is the first database of super-enhancers, in mouse and human genome. This database has been built with the explicit goal of providing a resource for further study of transcriptional control of cell identity, and meantime making the UI more responsive and user friendly.