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LEGE on HISAT2 Index Files Download ! (955 days ago): AWS registry https://registry.opendata.aws/jhu-indexes/
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Virus Bioinformatics Tools
By LEGE 4 days agoevirusbioinfc.notion.site - Bioinformatics tools play a crucial role in studying viruses, enabling researchers to analyze their genetic makeup, structure, function, and evolution. Here are some commonly used bioinformatics tools for virus...Minda: a tool for evaluating structural variant (SV) callers
By LEGE 28 days agogithub.com - Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set...Severus: a somatic structural variation (SV) caller for long reads
By LEGE 28 days agogithub.com - Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT). It is designed for matching tumor/normal analysis, supports multiple tumor samples, and produces accurate and complete somatic and germline calls. Severus...GraphPath: A graph attention model for molecular stratification with interpretability based on the...
By LEGE 31 days agogithub.com - Achieving accurate and interpretable clinical predictions requires paramount attention to thoroughly characterizing patients at both the molecular and biological pathway levels. In this paper, we present GraphPath, a biological knowledge-driven...ExRec: Exclusion of Recombined DNA
By LEGE 31 days agogithub.com - ExRec (Exclusion of Recombined DNA) is a Python pipeline that implements the four-gamete test to filter out recombined DNA sites from up to thousands of DNA sequence loci. The pipeline consists of five standalone applications: the first two convert...CGView.js is a Circular Genome Viewing tool
By LEGE 31 days agohttps://js.cgview.ca/ - CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView. CGView.js is the genome viewer of Proksee, an expert system for genome...Proksee
By LEGE 31 days agohttps://proksee.ca/ - Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file. Please Cite the Following Grant JR, Enns E, Marinier E,...R Package for PCA Analysis
By LEGE 34 days agorpubs.com - An R package for performing principal component analysis (PCA) of genomics data. The package performs PCA, generates the publication-ready plots, and identifies population-specific outlier individuals. The package can be accessed on...doubletrouble: identify duplicated genes from whole-genome protein sequences and classify
By LEGE 54 days agobioconductor.org - doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal...OMArk: software for proteome (protein-coding gene repertoire) quality assessment
By LEGE 66 days agogithub.com - OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence...
