2111 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureC...2109 days ago
mmgenome: Tools for extracting individual genomes from metagneomes
...e same time reproducible through the Rmarkdown format. The mmgenome R package also facilitates effortless i...hence should not be seen as "yet another binning method", but rather a package to integrate different binnin...2109 days ago
CBS Comparative Microbial Genomics group - BioTools download page
...esents a stand-alone interface for comparative microbial genomics. The package is a customized operating sys...r the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing th...2096 days ago
2070 days ago
funannotate: Eukaryotic Genome Annotation Pipeline
...unannotate is a genome prediction, annotation, and comparison software package. It was originally written to...over time to accomodate larger genomes. The impetus for this software package was to be able to accurately...2068 days ago
2045 days ago
vcfR: a package to manipulate and visualize VCF data in R
VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF file...2032 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
...LAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use...2027 days ago
ANItools web: a web tool for fast genome comparison within multiple bacterial strains
ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide ident...2012 days ago