Basic Deep

iVikodak



Meaningful inference, exploration and analysis of inferred

Functions of Microbiome

Features & Possibilities

iVikodak has been designed and developed with a vision to establish a benchmark for a structured and logical 'inference, exploration, analysis and visualization' of 16S derived functional potential of microbial communities. There are myriad of possibilites in 16S driven functional metagenomics space, and iVikodak makes a sincere effort to open-up all those avenues for the research community.

Co-inhabitance based functional inference

Microbes are expected to either co-metabolize in an environment or thrive independently of each other. Given these contexts of co-inhabitance between microbes, iVikodak uses two distinct algorithms - namely Co-Metabolism (CoM) and Independent Contributions (ICo) for inferring the functional potential of microbes.

Quorum based functional filtrations

It won't be just, if a pathway/function is inferred to be present in an environment, even if there are very few constituting genes/ enzymes available in the metagenomic environment. Given this context, gene/ enzyme quorum based filtration of functions is provided in iVikodak through PEC threshold based functional inference.

Contributor Profiling & Exploration

Each microbe is expected to have its distinct contribution towards one or more functions inferred in the environment. This information is crucial for a variety of exploratory and comaprative analyses. iVikodak makes it extremely easy for the end users to view, analyse and explore microbial contributions towards various functions (or functions of interest)

Function driven microbial interactions

A convention in the 16S based metagenomic analysis has been to probe co-occurence networks. iVikodak brings forward the concept of co-contribution networks (which are derived through analysis of functional correlations between various pairs of microbes, by probing their independent contributions). The networks so obtained, help in understanding microbial dynamics through a functional perspective

Deep Probing functions of interest

Whereas it is useful to have a general profile of all the functions inferred for the environment, a detailed probing of a particular function for one or more environments is often very useful for a biologically relevant exploration/ comparison of one or more environments. iVikodak, through a dedicated module named Local Mapper, enables a user to deeply probe the function(s) of interest in one or more environments

Multi-Environment probing and comparisons

iVikodak's capability to infer functions is not limited to a single environment. It can handle large scale of meta-data for multiple environments in a single execution, and also enable comaprisons across all environments through its specifically designed modules and algorithms

Interactive and Downloadable Visual Analytics

One of the highlights of iVikodak platform is in providing highly interactive and downloadable visualizations pertaining to various automated analyses in each and every module, for each and every metadata (and corresponding environments). This enables the ends users to have logical and meaningful insights into the functional aspects of the metagenomic environments they wish to explore

Ensemble of Textual Results

Understanding the requirement of performing independent analyses of various kinds, iVikodak provides an enriched ensemble of textual (downloadable) results in well structured directories. This includes results pertaining to functional inferences, as well as their automated analyses like Ordination, Core Profiling, Networks etc

Personal and Portable Dashboards

With its unique 10-character alphanumeric JOB ID driven job handling iVikodak without seeking any personal information. Coupled to that, each JOB ID is subsequently tagged to a personal Dashboard, which packages and presents all visualizations and results. The dashboards can be downloaded as unique '.dash files' which can be retained and shared by the end-users for future re-explorations. The 'dash files' can be uploaded to 'Recreator' module of iVikodak which recreates an entire dashboard using the unique dash file.

Analytics and Visualizations at a glance

iVikodak provides the end users with myriad of highly interactive and downloadable high-quality visualizations of various functional inferences and associated analytics. Each module of iVikodak, creates an personalized dashboard, which not only provides an ensemble of explorable textual results but numerous (relevant) visualizations for fast and meaninful analysis as well.

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Ordinations

JSD based PCoA

2D and 3D interactive ordination plots, visualizing the beta-diversity of functions across user-supplied meta data of environments

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Core Functions

Heatmaps of Core functions

Interactive heatmaps visualizing the consistently prevalent functions across user-supplied meta data of environments

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Top Functions

Box plots of Top Functions

Interactive box plots visualizing the Top functions at various hierarchies, across user-supplied meta data of environments

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Networks

Functional correlations based microbial interactions

Highly interactive, explorable and downloadable network graphs of functional correlation based microbial interactions (we have termed them as Co-contribution networks)

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Cladograms

Cladograms of differentiating functions

Differentiating functions (at all levels of hierarchy) derived using bootstrapped (BH corrected) wilcoxon & kruskal wallis tests are visualized using interactive and downloadable cladograms

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PEC Differentiators

Heatmaps of PEC Threshold based differentiating functions

Interactive and downloadable heatmaps representing 'a confident subset of differentiating functions' at various PEC Thresholds. Function observed to be differentiating at all PECs are most reliable markers

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Enzyme Profiles

Heatmaps of Enzyme Profiles

Interactive and downloadable heatmaps visualizing the abundance profiles of enzymes across all environments (as supplied in user-provided metadata) for a function of interest are generated.

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Contributors' Dendrobars

Dendrogram and Bar graphs clubbed in one

Interactive and downloadable 'Dendrobar' diagrams representing the taxonomic lineage and contribution of microbes towards a function of interest in all environments (as provided in metadata).

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KEGG Maps

Colored and 3D Pathway Maps

Local Mapper module provides for all environments (as supplied in metadata), keggmap files which can be used to generate colored and 3D pathway maps for the KEGG pathway of interest

Gallery of Some Results

Modules Exemplified

Click any of the below buttons to view sample dashboard of results for the corresponding module

Have a query/ suggestion?

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