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
@@ -1,36 +1,61 @@
UCSC Genome Browser Utilities
The following tools and utilities created by the UCSC Genome Browser Group are available for
public use:
-
Batch Coordinate Conversion (liftOver) -
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.
-
DNA Duster -
removes formatting characters and other non-sequence-related characters from an input sequence.
Offers several configuration options for the output format, including translated protein.
-
Protein
Duster - removes formatting characters and other non-sequence-related characters
from an input sequence. Offers several configuration options for the output format.
-
Phylogenetic Tree PNG Maker - creates a PNG image
from the phylogenetic tree specification given. Offers several configuration options for branch
lengths, normalized lengths, branch labels, legend etc.
-
Executable and
Source Code Downloads - executable and source code downloads of the Genome Browser,
Blat and liftOver.
+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:
+
+ -
+ RTracklayer -
+ R package to import genome annotations from our databases
+ - twobitreader - Python package to open
+ 2bit genome sequence files
+ - CruzDb -
+ Python package to load genome annotations from our servers
+ - ucsc-genomes-download -
+ Python package to download genome sequences from our servers
+
+ - trackhub -
+ Python package to manage files in our trackDb format
+
+ - WiggleTools -
+ C++ Unix command-line tool to work with bigWig files: combine, merge, scale, aggregate and many other operations.
+
+ - libBigWig -
+ A C library to read bigWig files, without a dependency on our source code
+
+ - -
+