Tools

Software packages and web resources

All bioinformatics tools, databases, and web servers developed or maintained across research programs.

RNA AnalysisActive

miPyRNA

An automated Python package for small RNA sequencing data analysis.

Small RNA AnalysisAutomated PipelineStatistical Analysis
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Variant AnalysisActive

SNVguru

An automated Python package for single nucleotide variation (SNV) analysis.

SNV DetectionVariant CallingAnnotation
View Repository
NGS AnalysisMaintained

pySeqRNA

An automated Python package for next-generation sequencing data analysis.

NGS PipelineQuality ControlDifferential Expression
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MetagenomicsActive

MetaNextViro

GitHub repository for MetaNextViro.

Viral AnalysisWorkflowResearch Tooling
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TranscriptomicsActive

TagSeq

GitHub repository for TagSeq.

Tag-based RNAAnalysis PipelineResearch Tooling
View Repository
Deep LearningStable

MINpred

A standalone alignment-free deep learning based tool for nitrogen mineralization enzyme classification.

Enzyme ClassificationDeep Learning ModelAlignment-free
View Download
Deep LearningStable

deepNEC

A standalone alignment-free deep learning based tool for nitrogen metabolism enzyme classification.

Metabolism AnalysisDeep Learning ModelAlignment-free
View Repository
14 resources

HPInet

database

A cereal crops and pathogen protein-protein interaction database.

host-pathogenprotein-interactioncereal-crops
Visit Resource

HuPoxNET

database

A database for human-monkeypox virus interactome.

host-pathogenvirusinteractome
Visit Resource

myDockDB

database

A multiple myeloma proteins and natural compounds docking web resource.

dockingmultiple-myelomanatural-compounds
Visit Resource

pySeqRNA

webserver

Complete documentation website for pySeqRNA package.

RNA-seqdocumentationgenomics
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ranchSATdb

database

A database of ranch animals microsatellite markers.

microsatelliteranch-animalsgenomics
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TritiKBdb

database

A host-pathogen interaction database for understanding Karnal Bunt disease infection mechanisms in wheat.

host-pathogenwheatdisease
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HuCoPIA

database

An atlas of human vs. SARS-CoV-2 interactome and comparative analysis with other Coronaviridae family viruses.

host-pathogenCOVID-19interactome
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deepNEC

webserver

An integrated web server platform for the prediction of nitrogen metabolism-related enzymes using deep learning.

deep-learningenzymesmetabolism
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deepHPI

webserver

A deep learning framework for the prediction of host-pathogen protein interactions and visualization.

deep-learninghost-pathogenprotein-interaction
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GreeningDB

database

A database of host-pathogen interactions and comparative omics of citrus and citrus greening disease (HLB).

host-pathogencitrusdisease
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covidTracker

webserver

A COVID-19 disease infection statistics tracker.

COVID-19disease-trackingstatistics
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legumeSSRdb

database

A legume species microsatellite markers database.

microsatellitelegumegenomics
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citSATdb

database

A citrus species microsatellite markers database.

microsatellitecitrusgenomics
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PRGminer

webserver

Deep learning based PR-genes prediction.

plant resistance geneR-genegenomics
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