7f2b62a70d0544af28cca22d3a7028dc164ec2c1 max Wed Feb 5 07:56:35 2020 -0800 documenting third part tools that use UCSC file formats or servers, refs #24666 diff --git src/hg/htdocs/util.html src/hg/htdocs/util.html index ee7e062..eb1a0cf 100755 --- src/hg/htdocs/util.html +++ src/hg/htdocs/util.html @@ -21,16 +21,41 @@ 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> <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> +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: +public use:</p> +<ul class="gbsNoBullet"> + <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://pypi.org/project/twobitreader/">twobitreader</a></strong> - Python package to open + 2bit genome sequence files</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://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://daler.github.io/trackhub/">trackhub</a></strong> - + Python package to manage files in our trackDb format + </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> + <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=""></a></strong> - + </li> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->