Uploads by Hiram
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This special page shows all uploaded files.
| Date | Name | Thumbnail | Size | Description | Versions |
|---|---|---|---|---|---|
| 20:48, 16 June 2010 | Ce2Ws120AltSpliceCustomTrack.txt (file) |  |
172 bytes | adding db=ce2 definition | 3 |
| 20:57, 16 June 2010 | Ce6Ws190AltSpliceCustomTrack.txt (file) | |
172 bytes | the custom track reference track line for ce6/WS190 alternative splice track | 1 |
| 20:47, 16 June 2010 | Ce4Ws140AltSpliceCustomTrack.txt (file) | |
194 bytes | adding db=ce4 definition | 2 |
| 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 |
| 18:31, 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 |
| 18:00, 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 |
| 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 |
| 18:06, 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 |
| 18:29, 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 |
| 18:07, 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 |
| 18:30, 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 |
| 17:17, 19 March 2015 | Create scores file control.txt (file) | |
653 bytes | Parameters from Bob Harris for lastz tuning procedure | 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 |
| 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 |
| 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 |
| 02:53, 6 April 2018 | ParasolInstall.sh.txt (file) | |
1 KB | adding git fetch of automation scripts into /data/scripts/ | 3 |
| 20:32, 25 September 2018 | NodeReport.sh.txt (file) | |
1 KB | add usage message and directory argument for result file | 4 |
| 23:34, 18 March 2015 | TopAll sh.txt (file) | |
2 KB | script used in lastz tuning procedure to run lastz_D on different sets of DNA sequences from query and target | 1 |
| 17:09, 19 March 2015 | SelectedFasta sh.txt (file) | |
2 KB | generalize the chrom.size creation and noMask option on fasta creation | 2 |
| 23:18, 18 March 2015 | MafScoreSizeScan pl.txt (file) | |
2 KB | script used to scan a MAF file to extract scores, sizes, and coverage statistics of each alignment block. Used in lastz tuning procedures. | 1 |
| 19:00, 10 August 2006 | TestCustomTrack.data.txt.gz (file) |  |
2 KB | Testing file upload feature. This is a custom track test file demonstrating all track types currently (August 2006) supported by the browser custom tracks. | 1 |
| 16:43, 24 June 2011 | ExtractRepeats.txt (file) | |
2 KB | Small perl script used to extract lineage specific repeats from RepeatMasker .out files | 1 |
| 18:00, 11 June 2007 | CleanHgCentral pl.txt (file) | |
2 KB | PERL cleaner script for userDb and sessionDb tables in hgcentral | 1 |
| 05:04, 13 March 2013 | BlatJob.csh.txt (file) | |
2 KB | script to use for the same species lift over procedure run.blat/ step 1 | 1 |
| 17:10, 19 March 2015 | AdjustSizes pl.txt (file) | |
3 KB | chrom.sizes files are now expected to exist as created by selectedFasta.sh | 2 |
| 22:47, 13 May 2008 | EmbedURL php.txt (file) | |
3 KB | UCSC modified EmbedURL extension code php file. Adds scrolling and frameborder options, and defaults width and height to 100% and 500 | 1 |
| 17:10, 26 September 2018 | InitParasol.sh.txt (file) | |
3 KB | less restrictive subnet specification and separate hub/node logs in ./logs/ directory | 3 |
| 21:54, 1 October 2018 | AwsAttachVolume.sh.txt (file) | |
4 KB | Script for AWS instance initialization to attach a data volume to a running instance. Used in the startParaHub.sh script upon starting the machine. | 1 |
| 17:42, 11 July 2018 | OpenStackParaNodeSetup.sh.template.txt (file) | |
4 KB | correctly fixup /mnt filesystem for broken openstack installation, and mount /mnt/data from the hub | 2 |
| 17:14, 19 March 2015 | Expand scores file py.txt (file) | |
4 KB | Script created by Bob Harris for lastz tuning operations | 1 |
| 16:39, 18 September 2007 | Mm8 mm9.intronSize.png (file) |  |
5 KB | Mouse mm8 and mm9 intron size histogram, to size 50 nucleotides | 2 |
| 16:46, 18 September 2007 | Hg17 hg18.intronSize.png (file) |  |
5 KB | Human hg17 and hg18 intron size histogram to size 50 nucleotides | 2 |
| 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 |
| 19:24, 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 |
| 05:43, 13 March 2013 | SameSpeciesChainNet.sh.txt (file) | |
5 KB | Same species lift over, step 2 of 2, chain/net the blat psl results together into the result file | 1 |
| 16:36, 18 September 2007 | Mm8 mm9.exonCount.png (file) |  |
5 KB | Mouse mm8 and mm9 exon count by size histogram, to size 30 nucleotides | 2 |
| 16:43, 18 September 2007 | Hg17 hg18.exonCount.png (file) |  |
5 KB | Human hg17 and hg18, exon count by size histogram, to size 30 nucleotides | 2 |
| 18:28, 30 October 2007 | PhastCons30way.png (file) |  |
5 KB | Mouse Mm9 30-way conservation phastCons histogram plot for the track data phastCons30way | 1 |
| 22:03, 3 December 2007 | Mm9Placental.png (file) |  |
5 KB | Mm9 alternative phastCons data histogram, Placentals, =mm9,rn4,cavPor2,oryCun1,hg18,panTro2,ponAbe2,rheMac2,calJac1,otoGar1,tupBel1,sorAra1,eriEur1,canFam2,felCat3,equCab1,bosTau3,dasNov1,loxAfr1,echTel1 | 3 |
| 22:04, 3 December 2007 | Mm9Euarchontoglires.png (file) |  |
5 KB | Mm9 alternative phastCons data histogram, Euarchontoglires, mm9,rn4,cavPor2,oryCun1,hg18,panTro2,ponAbe2,rheMac2,calJac1,otoGar1,tupBel1 | 3 |
| 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 |
| 16:41, 18 September 2007 | Mm8 mm9.intronsTo170.png (file) |  |
5 KB | Mouse mm8 and mm9 intron size histogram, to size 170 nucleotides | 2 |
| 16:38, 18 September 2007 | Mm8 mm9.exonSize.png (file) |  |
5 KB | Mouse mm8 and mm9 exon size histogram, to size 50 nucleotides | 2 |
| 16:46, 18 September 2007 | Hg17 hg18.intronsTo170.png (file) |  |
5 KB | Human hg17 and hg18 intron size to 170 nucleotides | 2 |
| 16:45, 18 September 2007 | Hg17 hg18.exonSize.png (file) |  |
5 KB | Human hg17 and hg18 exon size histogram, to size 50 nucleotides | 2 |
| 04:57, 13 March 2013 | SameSpeciesBlatSetup.sh.txt (file) | |
6 KB | First step in the same species lift over procedure, set up for blat run, adding 11.ooc file construction for blat | 2 |
| 17:43, 19 March 2015 | MatrixSummary pl.txt (file) | |
6 KB | used in lastz tuning procedure, examines output of the four lastz_D outputs to survey the differences | 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 |
| 19:37, 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 |
| 16:33, 18 September 2007 | Mm8 mm9 exonsTo300.png (file) |  |
6 KB | Mouse mm8 and mm9 exon size histogram to size 300 nucleotides | 2 |
