Rahul Nayak
A Bioinformatician
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GeneOverlap: An R package to test and visualize gene overlaps
By Jit 2156 days agobioconductor.org - Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose,...CONTIGuator !
By BioStar 1875 days agosourceforge.net - CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).NearHGT
By Jit 3074 days agojournals.plos.org - Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the...PASA: Gene Structure Annotation and Analysis
By biogeek 2522 days agopasapipeline.github.io - PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation...WEGO : simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation...
By BioStar 1684 days agowego.genomics.org.cn - WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2364 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 1591 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 917 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 3666 days agoan R package for analysing ontologies and protein domain annotationsRCircos: an R package for Circos 2D track plots
By Jit 3107 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...
