Uploads by Hiram

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Date Name Thumbnail Size Description Versions
20:13, 22 March 2011 29mammalsConstrainedElements omega branchLength.bw (file) 54.38 MB gwUploadFile upload 1
20:43, 21 March 2011 29mammalsConstraintStructure.bw (file) 219 KB test upload 1
20:42, 21 March 2011 29mammalsMotifInstances.bb (file) 38.25 MB test upload 1
20:41, 21 March 2011 29mammalsExaptedElements.bb (file) 3.51 MB test upload 1
20:36, 21 March 2011 29mammals2xHARs.bb (file) 45 KB test upload 1
20:33, 21 March 2011 29mammals2xPARs.bb (file) 45 KB test upload 1
20:31, 21 March 2011 29mammalsNovelExons.bb (file) 411 KB test upload 1
23:44, 25 January 2011 ConstructLiftFile pl.txt (file) 1 KB Given a partition list from partitionSequence.pl and a chrom.sizes file, this perl script will construct a lift file to be used to lift psl query and target results from those partitions after a lastz alignment. 1
17:28, 6 January 2011 BME230 Winter 2011.ppt (file) 6.25 MB Hiram Clawson, BME 230 lecture, 06 January 2011, introduction to the genome browser and programming with the kent source tree. 1
18:04, 15 September 2010 Knetfile hooks.0.1.7.patch (file) 13 KB Patch to samtools-0.1.7 to enable UCSC network functions and caching for remote BAM file access 1
18:03, 15 September 2010 Knetfile hooks.0.1.8.patch (file) 16 KB Patch to samtools-0.1.8 to enable UCSC network functions and caching for remote BAM file access 1
20:57, 16 June 2010 Ce6Ws190AltSpliceCustomTrack.txt (file) 172 bytes the custom track reference track line for ce6/WS190 alternative splice track 1
20:55, 16 June 2010 Ce6.altSplice.bb (file) 213 KB Alternate splice sites lifted from WS170 track to WS190 coordinates from IntronWS120 file: altsplice.EX.html) 1
20:48, 16 June 2010 Ce2Ws120AltSpliceCustomTrack.txt (file) 172 bytes adding db=ce2 definition 3
20:47, 16 June 2010 Ce4Ws140AltSpliceCustomTrack.txt (file) 194 bytes adding db=ce4 definition 2
20:44, 16 June 2010 Ce4.altSplice.bb (file) 213 KB Alternate splice sites lifted from WS120 track to WS170 coordinates from IntronWS120 file: altsplice.EX.html) 1
20:39, 16 June 2010 Ce2.altSplice.bb (file) 212 KB Alternate splice sites from IntronWS120 file: altsplice.EX.html 4
18:31, 19 March 2010 Hg17.customText.UCSC GGM SpecificCGIs.txt (file) 257 bytes customText track definition for hg17 custom track: CGIs (specific) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.67 1
18:30, 19 March 2010 Hg17.customText.UCSC GGM SensitiveCGIs.txt (file) 296 bytes customText track definition for hg17 custom track: CGIs (sensitive) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.33 1
18:29, 19 March 2010 Hg17.customText.UCSC GGM CombinedEpigeneticScore.txt (file) 272 bytes customText track definition for hg17 custom track: Epigenetic score - Combined epigenetic score (high scores correspond to bona fide CpG islands) 1
18:28, 19 March 2010 Hg17.customText.UCSC GGM BalancedCGIs.txt (file) 257 bytes customText track definition for hg17 custom track: CGIs (balanced) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.5 1
18:27, 19 March 2010 Hg17.customText.UCSC GGM All.txt (file) 1 KB customText track definition for all five data sets UCSC GGM CpGs 1
18:25, 19 March 2010 Hg17.UCSC GGM SpecificCGIs.bb (file) 178 KB bigBed data for hg17 custom track: CGIs (specific) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.67 1
18:23, 19 March 2010 Hg17.UCSC GGM SensitiveCGIs.bb (file) 686 KB bigBed data for hg17 custom track: CGIs (sensitive) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.33 1
18:22, 19 March 2010 Hg17.UCSC GGM OptimizedScore.bb (file) 1.99 MB bigBed data for hg17 custom track: Optimized score - Optimized score (high scores correspond to bona fide CpG islands 1
18:21, 19 March 2010 Hg17.UCSC GGM CombinedEpigeneticScore.bb (file) 2.02 MB bigBed data for hg17 custom track: Epigenetic score - Combined epigenetic score (high scores correspond to bona fide CpG islands) 1
18:19, 19 March 2010 Hg17.UCSC GGM BalancedCGIs.bb (file) 389 KB bigBed data for hg17 custom track: CGIs (balanced) Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.5 1
18:07, 19 March 2010 Hg18.customText.UCSC GGM CombinedEpigeneticScore.txt (file) 272 bytes customText for hg18 custom track: Combined epigenetic score (high scores correspond to bona fide CpG islands) 1
18:06, 19 March 2010 Hg18.customText.UCSC GGM SensitiveCGIs.txt (file) 259 bytes customText for hg18 custom track: Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.33 1
18:05, 19 March 2010 Hg18.customText.UCSC GGM SpecificCGIs.txt (file) 257 bytes customText for hg18 custom track: Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.67 1
18:00, 19 March 2010 Hg18.customText.UCSC GGM BalancedCGIs.txt (file) 257 bytes customText track definition for hg18 custom track: Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.5 1
17:54, 19 March 2010 Hg18.customText.UCSC GGM All.txt (file) 1 KB customText track statements to load all five UCSC_GGM CpG custom tracks 2
17:30, 19 March 2010 Hg18.UCSC GGM SpecificCGIs.bb (file) 178 KB bigBed data for hg18 custom track: Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.67 1
17:30, 19 March 2010 Hg18.UCSC GGM SensitiveCGIs.bb (file) 686 KB bigBed data for custom track: Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.33 1
17:28, 19 March 2010 Hg18.UCSC GGM OptimizedScore.bb (file) 1.99 MB bigBed data for hg18 custom track: Optimized score (high scores correspond to bona fide CpG islands) 1
17:28, 19 March 2010 Hg18.UCSC GGM CombinedEpigeneticScore.bb (file) 2.02 MB bigBed data for hg18 custom track: Combined epigenetic score (high scores correspond to bona fide CpG islands) 1
17:27, 19 March 2010 Hg18.UCSC GGM BalancedCGIs.bb (file) 389 KB bigBed data for custom track of Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.5 1
22:38, 5 January 2010 BME230 Winter 2010.ppt (file) 6.33 MB Hiram Clawson, BME 230 lecture, 05,07 January 2009, introduction to the genome browser and programming with the kent source tree. 1
19:25, 1 December 2009 PhastCons46wayPrimates.histogram.png (file) 5 KB 46-way conservation track on human genome browser hg19. phastCons histogram data for the primates subset 1
19:24, 1 December 2009 PhastCons46wayPlacental.histogram.png (file) 5 KB 46-way conservation track on human genome browser hg19. phastCons histogram data for all placental mammal subset 1
19:24, 1 December 2009 PhastCons46way.histogram.png (file) 5 KB 46-way conservation track on human genome browser hg19. phastCons histogram data for all 46 vertebrates 1
19:37, 30 November 2009 PhyloP46wayPrimates.histogram.png (file) 6 KB 46-way conservation track on human genome browser hg19. phyloP histogram data for all primates subset 1
19:36, 30 November 2009 PhyloP46wayPlacental.histogram.png (file) 6 KB 46-way conservation track on human genome browser hg19. phyloP histogram data for all placental mammal subset 1
19:35, 30 November 2009 PhyloP46way.histogram.png (file) 6 KB 46-way conservation track on human genome browser hg19. phyloP histogram data for all 46 vertebrates 1
22:14, 14 October 2009 MonsatoIntroduction Oct2009.pdf (file) 8.37 MB Montsanto Introduction, Genecats 14 Oct 2009 1
20:46, 14 October 2009 Genecats 2009 10 14.pptx (file) 86 KB Building the kent source tree and a UCSC genome browser assembly, Genecats 2009-10-14 Hiram Clawson 1
20:46, 14 October 2009 Genecats 2009 10 14.ppt (file) 141 KB Building the kent source tree and a UCSC genome browser assembly, Genecats 2009-10-14 Hiram Clawson 1
22:28, 17 September 2009 MultAlign.jpg (file) 14 KB Example tool tip pop up image 1
18:46, 29 July 2009 SvnForGb.pdf (file) 171 KB Mark's presentation to 2009-07-29 genecats, review of SVN subversion and how it could replace CVS 1
18:27, 25 March 2009 Teal Day 05.jpg (file) 1.02 MB Trying to recover a mysterious bogus file directory link 1
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