Rahul Nayak
A Bioinformatician
Latest comments
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (838 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (838 days ago): CheckM for...
- Rahul Nayak on CrossMap: program for genome coordinates conversion between different assemblies (1033 days ago): https://www.researchgate.net/publication/357925950_FastRemap_A_Tool_for_Quickly_...
- Rahul Nayak on RGFA: powerful and convenient handling of assembly graphs (1769 days ago): The Graphical Fragment Assembly (GFA) is a proposed format which allow to...
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Genome, Assembly, reads, analysis, NGS, de novo, Tools, Bioinformatics, tool, visualization, data, R, sequencing, Pipeline, Computational Biology, Long, Assemblies, fast, AligNment, annotation, assembler, genomes, Software, MUltiple, Python, genes, database, Genomics, Tutorial, Education, scaffolding, transcriptome, Nanopore, fastq, Perl, Merging, Solution, Tree, Network, Resolution, U-Plot, gene, Bacteria, gap, Genomic, structure, Elements, mapping, Suite, system
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Rahul Nayak's bookmarks
Seq: A high-performance, Pythonic language for bioinformatics
By Rahul Nayak 1827 days agohttps://seq-lang.org - Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing...radar charts with ggplot2
By Rahul Nayak 1894 days agogithub.com - ggradar allows you to build radar charts with ggplot2. This package is based on Paul Williamson’s code, with new aesthetics and compatibility with ggplot2 2.0. It was inspired by d3radaR, an htmlwidget built...Retrieving Taxonomic Information with R
By Rahul Nayak 1913 days ago Comments (2)cran.r-project.org - This vignette will introduce users to the retrieval of taxonomic information with myTAI. The taxonomy() function implemented in myTAI relies on the powerful package taxize. Nevertheless, taxonomic information retrieval...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 1967 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...ansible: Simple, agentless IT automation that anyone can use
By Rahul Nayak 2047 days agohttps://www.ansible.com/ - Ansible is a universal language, unraveling the mystery of how work gets done. Turn tough tasks into repeatable playbooks. Roll out enterprise-wide protocols with the push of a button. Give your team the tools to automate, solve, and share.dotPlotly: Generate an interactive dot plot from mummer or minimap alignments
By Rahul Nayak 2102 days agogithub.com - Create an interactive dot plot from mummer output OR PAF format R script that makes a plotly interactive and/or static (png/pdf) dot plot. Shiny app available for testingGRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research
By Rahul Nayak 2128 days agogithub.com - GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs....GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various...
By Rahul Nayak 2139 days agolce.biohpc.swmed.edu - GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information. It efficiently constructs gene...CViT: Chromosome Viewing Tool
By Rahul Nayak 2152 days agosourceforge.net - CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single...GenomeView: genome browser and annotation editor
By Rahul Nayak 2152 days agosourceforge.net - GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.This project has...
