Rahul Nayak
A Bioinformatician
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ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
By Jit 2065 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 1391 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 3441 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 2807 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 1346 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 2419 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 2107 days agoUseful resources to therapy, disease, drug and drug-target network dataJumboDB: tool for de Bruijn graph construction
By BioStar 1665 days agogithub.com - jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low error rate. JumboDB is not a genome assembler by itself but rather a subroutine that translates a set of reads into compressed de Bruijn...Basics of DESeq2: Differential Expression Made Simple
By LEGE 286 days agoDESeq2 is a powerful and widely-used R package that identifies differentially expressed genes (DEGs) from RNA-seq data. Whether you're comparing treated vs untreated samples, disease vs healthy conditions, or wild-type vs mutant strains, DESeq2...Tools for Differential expression analysis
By Abhi 1218 days ago Comments (1)the sequenced reads can be mapped to the organism’s genes to assess how differently the genes are expressed under the experimental circumstances as opposed to the control scenario. This is known as differential expression (DE) analysis
