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HiGlass: a tool for exploring genomic contact matrices and tracks.
...ploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a descr...lass can be run locally within a Docker container. The HiC data in the examples below is from Rao et al. (201...2169 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...rage-per-SNP) using above technologies combinations of the above technologies (e.g. scaffold long reads with Hi-C reads) See below for specific examples of command line options and b...2196 days ago
CGView - Circular Genome Viewer
...e labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. For examples of the various output types,...2160 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...a stand-alone app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/j...2151 days ago
Bokeh: An interactive visualization library that targets modern web browsers for presentation
...e interactive plots, dashboards, and data applications. To get started using Bokeh to make your visualizations, see the User Guide. To see examples of how you might use Bokeh wi...2109 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
...Canu, FALCON or FALCON-Unzip primary contigs) or on a phased-diploid assembly (i.e. FALCON-Unzip primary contigs + haplotigs). Here are two examples of how Purge Haplotigs c...1980 days ago
Genome Annotation using MAKER tutorial !
... GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort t...1977 days ago
UPhO: Scripts for homology and orthology assessment from genomic sequences.
...denfifier, a field separator, and sequence identifier. By default, the field separator is the character "|" but custom delimiters can be defined. Examples of trees to test UPhO are pro...1952 days ago
Patterns: a modeling tool dedicated to biological network modeling
It is designed to work with patterned data. Famous examples of problems related to patterned data are: recovering signals in networks after a stimulation (cascade network reverse engineering), analysing periodic signals.1759 days ago
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
...ery organism in UniProt. Please refer to the complete documentation at proteoclade.readthedocs.io for installation, a user's guide, and examples. https://journals.plos.org/p...1523 days ago
