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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (203 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (659 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (820 days ago): Sequencing coverage is defined as the average number of reads that covers...
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DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
By Rahul Nayak 1761 days agosysomics.com - DeepHiC is a GAN-based model for enhancing Hi-C data resolution. We developed this server for helping researchers to enhance their own low-resolution data by a few steps of clicks. Ab initio training could be performed according to our published...shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams
By Jit 1764 days agoyimingyu.shinyapps.io - shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package. To create single-genome plot by aligning genome data along all chromosomes of a single genome, go to...RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS...
By Surabhi Chaudhary 1765 days agogithub.com - RAINBOWR(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of GWAS as follows. Single-SNP GWAS with RGWAS.normal function SNP-set (or gene set) GWAS with RGWAS.multisnp function (which tests...Best Practices for Variant Calling with the GATK
By biogeek 1771 days agowww.broadinstitute.org - The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version...Juicebox: Visualization and analysis software for Hi-C data
By Jit 1772 days agogithub.com - Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is...BlobToolKit: A toolkit for genome assembly QC
By Jit 1773 days agoblobtoolkit.genomehubs.org - Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible...BioContainers
By Jit 1773 days agobiocontainers.pro - BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics packages (e.g conda) and containers (e.g docker, singularity). BioContainers is based on the popular...Kubernetes: open-source system for automating deployment, scaling, and management of containerized...
By BioStar 1773 days agohttps://kubernetes.io/ - It groups containers that make up an application into logical units for easy management and discovery. Kubernetes builds upon 15 years of experience of running production workloads at Google, combined with best-of-breed ideas and practices from...Nextflow: Data-driven computational pipelines
By BioStar 1774 days ago Comments (2)https://www.nextflow.io/ - Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. Its fluent DSL simplifies the implementation and the deployment of...Instructions for Creating Your Own R Package
By Jit 1774 days ago Comments (2)web.mit.edu - The following is a step-by-step guide to creating your own R package. Even beyond this course, youmay find this useful for storing functions you create for your own research or for editing existingR packages to suit your needs. This guide...
