Bioinformatics tools

I have developed (co-developed) the following bioinformatics tools:

  • DIPx: Pathway activation model for personalized prediction of drug synergy
  • MDREAM: A web-based tool of Monotherapy Drug Response prediction for acute myeloid leukemia patients
  • FuSeq_WES: A method for detection of fusion genes from DNA-sequencing data
  • DCSP: Discovery of Druggable Cancer-Specific Pathways
  • MAX: Quantification of mutant-allele expression in cancer from RNA sequencing data
  • Scasa: A method for quantifying isoform expression from single-cell RNA-seq data from tag-based sequencing methods such as 10x Genomics
  • Circall: A fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data
  • CircNetVis: A tool to analyze circular RNAs through circRNA:miRNA:mRNA interaction and circRNA: RNA-binding-protein (RBP) interaction.
  • XAEM: A method to accurately quantify isoform expression from multiple RNA-sequencing samples.
  • SCmut: A method to detect cell-level mutation from single-cell RNA-sequencing.
  • FuSeq: A fast method to discover fusion genes from paired-end RNA-seq data.
  • BPSC: An R package for model fitting and differential expression analyses of single-cell RNA-sequencing data.
  • ISOP: An R package for analysing isoform-level expression patterns in single-cell RNA-sequencing data.
  • BRCAsubtypes: An interactive webpage to discover subtype-specific isoforms in breast cancer data.
  • AMLSubtypeSpecificDiscovery: An R-shiny tool for discovery of subtype-specific genes in Acute Myeloid Leukemia.
  • speaq: An R package including a suite of informatics tools for spectral alignment and quantitative analysis of NMR metabolomic profile data.
  • speaq 2.0:  A complete workflow for high-throughput 1D NMR spectra processing and quantification

Others:

  • mascotParser: An R package for parsing for Mascot search results (PMF and MSMS)