Rahul Nayak
A Bioinformatician
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Katju Lab
TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and...Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
By Jit 2980 days agowww.sanger.ac.uk - Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases using variable order motif...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2835 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
By Jit 2062 days agogithub.com - ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in...GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
By Neel 1388 days agogithub.com - The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is...dcGOR
By Martin Jones 4136 days agoan R package for analysing ontologies and protein domain annotationsRCircos: an R package for Circos 2D track plots
By Jit 3577 days agobitbucket.org - RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It...UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties
By BioStar 2594 days agogithub.com - UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data,...R Package for PCA Analysis
By LEGE 712 days agorpubs.com - An R package for performing principal component analysis (PCA) of genomics data. The package performs PCA, generates the publication-ready plots, and identifies population-specific outlier individuals. The package can be accessed on...regioneR: an R package for the management and comparison of genomic regions
By Jit 2642 days agogattaca.imppc.org - Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework....
