Park Lab

The purpose of computing is insight, not numbers. (Richard Hamming)

Software

scDeepJointClust for refining cell subgroup definitions of single cells by jointly training on the gene expression and biological condition information (e.g., tumor or normal samples) with Z. Fan
causalDeepVASE for learning causal structure in clinical or molecular data based on a deep neural network model with Z. Fan
scMAPA for detecting alternative polyadenylation signals in single-cell RNA-Seq data with Bai
PRIMATA-APA for characterizing a novel biological feature representing the number of microRNA binding sites in the transcriptome data with Kim
geneEXPLORER for predict gene expression using long-range methylation for pan-cancer with Kim
MACPath for identifying ceRNA pathways from ceRNAs with S. Kim, W. Li, PLoS Comp. Bio. 2018
MAT3UTR for predicting trans effect of 3'UTR shortening with P. Ji, W. Li, Nat. Gen. 2018
MOABS for comparing DNA methylation analysis between experiments with D. Sun, Y. Xi, B. Rodriguez, T. Pan, M. Jeong, MA Goodell, W. Li, 2014
CPAT for estimating coding potential of transcripts with L. Wang, S. Wang, J-P Kocher, W. Li, 2013
ExactNumCI for calculating Exact Confidence Interval for binomial proportions with D. Sun, 2013
MURPAR for inferring a phylogenetic network from a collection of gene trees with L. Nakhleh, 2012
NEPAL for phylogenetic network construction using the maximum parsimony and maximum likelihood criteria with G. Jin and L. Nakhleh, 2010
SLS for phylogenetic tree search under the maximum parsimony criterion with T. Williams, 2006