Performs graph classification and regression by machine learning algorithms. Graphkernels is a package in R and Python with efficient C++ implementations of various graph kernels including the following prominent kernel families: (1) simple kernels between vertex and/or edge label histograms, (2) graphlet kernels, (3) random walk kernels, and (4) the Weisfeiler-Lehman graph kernel.
Allows R users to generate Graphical User Interfaces (GUIs) for R scripts. RGG is a general GUI framework for R that consists of two parts: an XML based GUI definition language and a GUI engine. It is available both as a stand-alone software (RGGRunner) and as a plug-in for JGR. The software can be used to make biostatistical and bioinformatical solutions directly available for routine applications.
Generates interactive graphs in R. RJSplot contributes to the development of interactive visualization packages in R oriented toward computational biology research. The software implements 16 interactive graphical representations. It provides a dynamic and customizable visualization and allows actions such as browsing, movement, zoom adjustment, viewing values, or identifying variables. It can be used to allow a comprehensive visualization of information and an improved diffusion of scientific results.
Designed to integrate the major strengths of R and Cytoscape environments by providing a general Java to R interface. By linking these two environments, Cyrface allows one to use Cytoscape as a graphical user interface for R packages. It also enables Cytoscape apps to access the wealth of methods implemented in R. Cyrface is now compatible with Cytoscape 3.
Provides several tools for specialized analysis of animal social networks. Asnipe offers also access to other tools for more general analysis of network structure. This software can (1) define a group by individual matrix, (2) generate an association matrix from observations of individuals co-occuring in time and space, (3) perform permutation tests on the observation stream or (4) calculate lagged association rates between individuals or classes of individuals.
Provides a single destination for your Shiny applications, R Markdown documents, interactive HTML widgets, static plots, and more. RStudio Connect empowers analysts to share and manage the content created in R. Users of the RStudio IDE can publish content to the application with the click of a button and immediately be able to manage that content from a user-friendly web application. RStudio Connect is designed to bring the power of data science.
An easy-to-use statistical software with more 200 statistical tests, procedures and graphs. MedCalc allows to perform data management, ROC curve analysis, method comparison and method evaluation including Bland and Altman plot, Passing and Bablok, and Deming regression, and a lot of graphs.
Allows users to handle and remove packages from a given library. Packrat enhances user project directory by storing its package dependencies inside it. This tool tries to make projects more: (1) isolated, (2) portable, (3) reproducible.
Provides method for astrochronologic testing, astronomical time scale construction, and time series analysis. Astrochron can be used for statistical analysis and modeling routines that are relevant to paleoclimate analysis.
Gene fusion detection in Plants
Fusion transcripts (i.e., chimeric RNAs) resulting from gene fusions are well known in case of human. But, in plants, this phenomenon is not yet explored. We are planning to discover the fusion transcripts/gene fusions in different type of plants by using RNA-Seq datasets. Further, we are planning to understand the mechanism of gene fusion formation and significance of fusions in plants.
Whole genome and transcriptome sequencing data analysis of Plants
In this era of Next Generation Sequencing (NGS), there is huge amount of sequencing data available in the public domain. Any novel finding from these available datasets is major challenge for a computational biologist. We are interested in the analysis of whole genome and transcriptome sequencing data of different plants to fetch out the useful information from those datasets, with the help of bioinformatics tools. Currently, we are planning to study the gene clusters of secondary metabolite pathways in different plants.
Development of webservers, databases and computational pipelines for plant research
Development of database is necessary to compile and share the information with scientific community. We are dedicated to develop useful databases and webserver for plant research.
Another area of interest is to develop automated pipelines and tools for the analysis of high throughput genomics data, generated by NGS technologies.
Professional & Academic Background
Staff Scientist II (May 2017- present): National Institute of Plant Genome Research (NIPGR), New Delhi, India
Postdoctoral Research Associate (2015-2017): University Of Virginia, Charlottesville, VA, USA
Research Scientist (2014-2015): Sir Ganga Ram Hospital, New Delhi, India
PhD Bioinformatics (2009-2014): Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh under Jawaharlal Nehru University (JNU), New Delhi, India
M.Sc. Life Sciences (2007-2009): Jawaharlal Nehru University (JNU), New Delhi, India
B.Sc. Biotechnology (2004-2007): Jamia Millia Islamia (JMI), New Delhi, India
Awards and Fellowships
Junior and Senior Research Fellowship (2009-2014): Council of Scientific and Industrial Research (CSIR), New Delhi, India
GATE (Graduate Aptitude Test in Engineering): Qualified in years 2008 and 2009
Scientific Contributions/ Recognitions
Associate editor: Journal of Translational Medicine.
Editorial Board Member of Journal: Theoretical Biology and Medical Modelling.
Reviewer: PloS One, BMC Genomics, BMC Bioinformatics, BMC Biology, BMC Biotechnology, Frontiers in Physiology and several other journals.
Web Resources/ Databases (Developed/ Contributed)
A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer (http://www.imtech.res.in/raghava/cancertope/)
GenomeABC: A webserver for benchmarking of genome assemblers. (http://crdd.osdd.net/raghava/genomeabc/).
Genomics web portal page. (http://crdd.osdd.net/raghava/genomesrs/).
Map/Alignment module of CancerDr: Cancer Drug Resistance Database. (http://crdd.osdd.net/raghava/cancerdr/).
Short reads and contigs alignment module of PCMDB: Pancreatic cancer methylation database. (http://crdd.osdd.net/raghava/pcmdb/).
Burkholderia sp. SJ98 database. (http://crdd.osdd.net/raghava/genomesrs/burkholderia/).
Rhodococcus imtechensis RKJ300 database. (http://crdd.osdd.net/raghava/genomesrs/rkj300/).
Genotrick: A pipeline for whole genome assembly and annotation of Genomes (http://crdd.osdd.net/raghava/genomesrs/genotrick/)
Development of Debian packages in OSDDlinux: A Customized Operating System for Drug Discovery. (http://osddlinux.osdd.net/).
A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. (http://crdd.osdd.net/raghava/mtbveb/).