Results for "Maps"
Tags
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver optio...Tags: pbalign, maps, PacBio, reads, reference, sequences, alignments, BAM, NGS
2163 days ago
genoPlotR - plot gene and genome maps project!
genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files. Features Linear representation of several segments of DNA Comp...Tags: genoPlotR, plot, gene, genome, maps, project, R
1962 days ago
Leaflet: JavaScript libraries for interactive maps
Leaflet is one of the most popular open-source JavaScript libraries for interactive maps. Features Interactive panning/zooming Compose maps using arbitrary combinations of: Map tiles Markers Polygons Lines Popups GeoJSON Create maps right from the R console or RStudio Embe...Tags: Leaflet, JavaScript, libraries, interactive, maps
1537 days ago
- Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assemb...
Tags: Chromonomer, tool, repairing, enhancing, assembled, genomes, integration, genetic, maps, conserved, synteny
1530 days ago
chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
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 to get the latest development version: pip3 in...Tags: chromosight, Computer, vision, program, pattern, recognition, chromosome, Hi-C, contact, maps
1495 days ago
gggenes: a ggplot2 extension for drawing gene arrow maps.
Install the stable version of gggenes from CRAN: install.packages("gggenes") If you want the development version, install it from GitHub: devtools::install_github("wilkox/gggenes") More at https://github.com/wilkox/gggenesTags: gggenes, ggplot2, extension, drawing, gene, arrow, maps
1423 days ago
Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
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 standalone tool that takes two genome assemblies ...Tags: Liftoff, accurate, tool, maps, annotations, GFF, GTF, assemblies
1395 days ago
ANGES: reconstructing ANcestral GEnomeS maps
This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes. Download Program, version 1.01 (July 10, 2012, documentation updated in August 2014) Examples with results (featured ancestors: boreoeutherian,...Tags: Reconstruction, Ancestral, Genomes, Maps, ANGES
2535 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available at: http://shendurelab.github.io/LACHESIS. Manusc...Tags: LACHESIS, Genome, Assembly, Hi-C, Contact, Probability, Maps, Genome, Assembly
2174 days ago
