Rahul Nayak
A Bioinformatician
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The Tree That Learned to Read Genomes
By BioStar 30 days agoA recent study by Webster and Chapman introduces Buscogeny, an open-source bioinformatics pipeline designed to make this process easier. The tool uses BUSCO (Benchmarking Universal Single-Copy Orthologs), which identifies conserved genes that are...Introduction to programming. Write short programs that generate graphics and animation.
By Ram Yash Pal 4440 days agoShort programs that generate graphics and animation.BEAP: Blast Extension and Assembly Program
By Shruti Paniwala 3043 days agowww.animalgenome.org - The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...Charpak exchange program
The scholarship is designed for Indian students from all fields and streams of study, enrolled in an Indian institution at the Bachelors or Master’s degree level, who wish to undertake a study exchange semester programme in France (for a period of...MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
By Poonam Mahapatra 3052 days agowww.fish-evol.com - MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutorial I will analyze an easy...DISTRUCT: a program for the graphical display of population structure
By Abhimanyu Singh 2757 days agorosenberglab.stanford.edu - distruct is a program that can be used to graphically display results produced by the genetic clustering program structure or by other similar programs. The figures produced by distructdisplay individual membership coefficients...chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
By Jit 2392 days agogithub.com - Python package to detect chromatin loops (and other patterns) in Hi-C contact maps. Stable version with pip: pip3 install --user chromosight Stable version with conda: conda install -c bioconda -c conda-forge chromosight or, if you want...SuRankCo: supervised ranking of contigs in de novo assemblies
By Neel 3426 days agosourceforge.net - SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2293 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...Syri compares alignments between two chromosome-level assemblies and identifies synteny and...
By Shruti Paniwala 1593 days agogithub.com - Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
