7ca00d20d2c5c137d78f47d364b4d5be09acfb15 dschmelt Thu Mar 25 17:03:26 2021 -0700 Stashing 2 tools and documenting others for refs #27278 diff --git src/hg/htdocs/util.html src/hg/htdocs/util.html index 33e4857..79dc196 100755 --- src/hg/htdocs/util.html +++ src/hg/htdocs/util.html @@ -1,80 +1,104 @@ <!DOCTYPE html> -<!--#set var="TITLE" value="Genome Browser Utilities" --> +<!--#set var="TITLE" value="Other Tools - UCSC Genome Browser" --> <!--#set var="ROOT" value="." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> -<h1>UCSC Genome Browser Utilities</h1> +<h1>Other Tools from the UCSC Genome Browser</h1> <p> -The following tools and utilities created by the UCSC Genome Browser Group are available for -public use:</p> +The UCSC Genome Browser team develops and updates the following main tools: +the <a href="../cgi-bin/hgTracks">Genome Browser</a>, +<a href="../cgi-bin/hgBlat">BLAT</a>, <a href="../cgi-bin/hgPcr">In-Silico PCR</a>, +<a href="../cgi-bin/hgTables">Table Browser</a>, and <a href="../cgi-bin/hgLiftOver">LiftOver</a>. +We maintain the following less-used tools: <a href="../cgi-bin/hgNear">Gene Sorter</a>, +<a href="../cgi-bin/hgGenome">Genome Graphs</a>, and +<a href="../cgi-bin/hgIntegrator">Data Integrator</a>. +These are available from the "Tools" dropdown menu at the top of the site.</p> + +<p> +We also offer command-line utilities for many file conversions and basic bioinformatics functions. +You can learn more and download these utilities through the +<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">utilities section</a> +of our downloads page.</p> + +<p> +The following tools and utilities created by the UCSC Genome Browser Group are also available +for public use:</p> <ul class="gbsNoBullet"> <li> - <strong><a href="cgi-bin/hgLiftOver">Batch Coordinate Conversion (liftOver)</a></strong> - - converts genome coordinates and genome annotation files between assemblies. The current version - supports both forward and reverse conversions, as well as conversions between selected - species.</li> + <strong><a href="../cgi-bin/hgPhyloPlace">UShER</a> (for SARS-CoV-2 only)</strong> - + allows placement of SARS-CoV-2 sequences onto existing phylogenetic trees for tracing strains + and transmission events.</li> + <li> + <strong><a title="Explore gene/protein interactions and pathways" + href="../cgi-bin/hgGeneGraph">Gene Interactions</a></strong> - + displays a gene interaction and pathway graph based on data from curated protein-interaction + databases and text mining of PubMed abstracts.</li> + <li> + <strong><a id="visiGeneMenuLink" href="../cgi-bin/hgVisiGene">VisiGene</a></strong> - + displays high-quality images of in-situ mouse and frogs with gene mRNA hybridization + probes and transcription factors.</li> <li> <strong><a href="http://users.soe.ucsc.edu/~kent/dnaDust/dnadust.html">DNA Duster</a></strong> - removes formatting characters and other non-sequence-related characters from an input sequence. Offers several configuration options for the output format, including translated protein.</li> <li> <strong><a href="http://users.soe.ucsc.edu/~kent/protDust/protDust.html">Protein Duster</a></strong> - removes formatting characters and other non-sequence-related characters from an input sequence. Offers several configuration options for the output format.</li> <li> <strong><a href="cgi-bin/phyloPng">Phylogenetic Tree PNG Maker</a></strong> - creates a PNG image - from the phylogenetic tree specification given. Offers several configuration options for branch - lengths, normalized lengths, branch labels, legend etc.</li> + from phylogenetic tree specification given; several configuration options for branch + lengths, normalized lengths, branch labels, legend, etc.</li> <li> <strong><a href="http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads">Executable and Source Code Downloads</a></strong> - executable and source code downloads of the Genome Browser, Blat and liftOver.</li> </ul> </p> <p> The following tools and utilities created by outside groups may be helpful when working with our file formats and the genome annotation databases that we provide. References to these tools are provided for the benefit of our users. We are unable to support the use of externally developed tools; if you have questions or problems, please contact the developers of the tool directly. <ul class="gbsNoBullet"> <li><strong><a href="https://bedops.readthedocs.io/en/latest/">BEDOPS</a></strong> - A highly scalable and easily-parallelizable genome analysis toolkit </li> <li><strong><a href="https://bedtools.readthedocs.io/en/latest/">bedtools</a></strong> - A swiss-army knife of tools for a wide-range of genomics analysis tasks </li> <li><strong><a href="https://github.com/CRG-Barcelona/bwtool/wiki">bwtool</a></strong> - A command-line utility for bigWig files </li> <li><strong><a href="http://crossmap.sourceforge.net/">CrossMap</a></strong> - A program for genome coordinate conversion between different assemblies </li> <li><strong><a href="https://pypi.org/project/cruzdb/">CruzDb</a></strong> - Python package to load genome annotations from our servers </li> <li><strong><a href="https://github.com/dpryan79/libBigWig">libBigWig</a></strong> - A C library to read bigWig files, without a dependency on our source code </li> <li><strong><a href="https://github.com/Gaius-Augustus/MakeHub">MakeHub</a></strong> - Python tool to build assembly hub files for new genomes </li> <li><strong><a href="https://bioconductor.org/packages/release/bioc/html/rtracklayer.html">RTracklayer</a></strong> - R package to import genome annotations from our databases </li> <li><strong><a href="https://daler.github.io/trackhub/">trackhub</a></strong> - Python package to manage files in our trackDb format </li> <li><strong><a href="https://pypi.org/project/twobitreader/">twobitreader</a></strong> - Python package to open 2bit genome sequence files </li> <li><strong><a href="https://pypi.org/project/ucsc-genomes-downloader/">ucsc-genomes-download</a></strong> - Python package to download genome sequences from our servers </li> <li><strong><a href="https://github.com/Ensembl/WiggleTools">WiggleTools</a></strong> - C++ Unix command-line tool to work with bigWig files: combine, merge, scale, aggregate and many other operations </li> </ul> </p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->