Rahul Nayak
A Bioinformatician
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Tigers genome sequenced
By Rahul Agarwal 4243 days agoOnly 4.4 percent DNA difference between Tiger and house catsEuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer...
By Surabhi Chaudhary 2546 days agobmcgenomics.biomedcentral.com - SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in...EGAD: Ultra-fast functional analysis of gene networks
By Rahul Nayak 2330 days agogithub.com - With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficient tools to calculate functional properties in networks based on the guilt-by-association principle. These allow rapid controlled...ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
By Jit 1752 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 1078 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...AccNET
By Jitendra Narayan 3128 days agosourceforge.net - AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET...NAViGaTOR: Network Analysis, Visualization and Graphing Toronto
By Rahul Nayak 2494 days ago142.150.188.236 - NAViGaTOR – Network Analysis, Visualization, & Graphing TORonto is a software system for scaleable visualizing and analyzing networks. The current version, NAViGaTOR 3, increases modularity, improves scaleability, extends input/output...JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges
By Shruti Paniwala 1033 days agogithub.com - This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine...Patterns: a modeling tool dedicated to biological network modeling
By Abhimanyu Singh 2106 days ago Comments (1)github.com - It is designed to work with patterned data. Famous examples of problems related to patterned data are: recovering signals in networks after a stimulation (cascade network reverse engineering), analysing periodic signals.Useful links to therapy, disease, drug and drug-target network data:
By Jit 1794 days agoUseful resources to therapy, disease, drug and drug-target network data
