Activity for David Nix

  • David Nix David Nix posted a comment on ticket #1

    OK, must install numpy to get CrossMap to run. pip install numpy

  • David Nix David Nix posted a comment on ticket #1

    Downloaded bx-python-0.7.3.tar.gz, installed via pip: pip install bx-python-0.7.3.tar.gz --upgrade Still getting ImportError: No module named bigwig_file

  • David Nix David Nix created a blog post

    USeq has moved to GitHub

  • David Nix David Nix committed [r308]

    Just modified the bed file output to contain th...

  • David Nix David Nix committed [r307]

    Big refactoring of the molecular barcode consen...

  • David Nix David Nix committed [r306]

    A bit of package rearrangements to accomidate t...

  • David Nix David Nix committed [r305]

    Lots of mods and new apps. More tweaks to the j...

  • David Nix David Nix committed [r304]

    Added ability to parse multi sample mpileup files

  • David Nix David Nix committed [r303]

    Hmm, can't seem to upload a release to SF's Fil...

  • David Nix David Nix committed [r302]

    Sam2USeq

  • David Nix David Nix committed [r301]

    Lots of mods related to filtering sam alignment...

  • David Nix David Nix committed [r300]

    Made a variety of modifications to support a ne...

  • David Nix David Nix committed [r299]

    Whole lot of mods and apps related to Bam QC, E...

  • David Nix David Nix committed [r297]

    Sam2USeq: Fixed an issue where chromData from t...

  • David Nix David Nix committed [r296]

    OK:

  • David Nix David Nix committed [r293]

    Added functionality to PoReCNV to join adjacent...

  • David Nix David Nix committed [r292]

    Fixed an issue with PoReCNV where the last chro...

  • David Nix David Nix committed [r289]

    Dropped support for unsorted sam.gz files, this...

  • David Nix David Nix committed [r288]

    Lots of mods to the individual VCF parsers to s...

  • David Nix David Nix committed [r287]

    Fixed an issue with the convertSangerQualitySco...

  • David Nix David Nix committed [r286]

    Finalized the normal exome CNV discovery app. M...

  • David Nix David Nix committed [r285]

    Added threading to the cnv app.

  • David Nix David Nix committed [r284]

    Lots of mods, see the release notes for 8.8.9.

  • David Nix David Nix committed [r282]

    Updated release notes for 8.8.9 release.

  • David Nix David Nix committed [r281]

    AllelicExpressionDetector - cleaned up code

  • David Nix David Nix committed [r280]

    Added option to keep duplicate marked alignment...

  • David Nix David Nix committed [r279]

    Fixed an issue with the JavaxComOrgInfoNetClass...

  • David Nix David Nix committed [r277]

    Fixed a major bug where variants were not being...

  • David Nix David Nix committed [r276]

    Fixed and issue with replacing the QUALity valu...

  • David Nix David Nix committed [r275]

    Added changes and apps to support BamQC for the...

  • David Nix David Nix committed [r273]

    Lots of mods related to splice site identificat...

  • David Nix David Nix committed [r271]

    Lots of mods....

  • David Nix David Nix committed [r270]

    Adding app to cluster samples in a multi sample...

  • David Nix David Nix committed [r268]

    Lots of mods:

  • David Nix David Nix committed [r267]

    Added option to filter vcfs by region, cleaned ...

  • David Nix David Nix created ticket #266

    Can't launch IGB after modifying igb-5GB.jnlp

  • David Nix David Nix committed [r265]

    Added new app to randomly split sam files, mods...

  • David Nix David Nix committed [r263]

    Added new app for MergingSam files, a catch for...

  • David Nix David Nix committed [r261]

    Lots of clean up of the documentation and addit...

  • David Nix David Nix committed [r259]

    Added lates changes to releaseNotes.txt

  • David Nix David Nix committed [r258]

    Lots of mods to Telescriptor and related classe...

  • David Nix David Nix committed [r256]

    Latest release notes

  • David Nix David Nix committed [r255]

    Adding in changes for Misc and Num.

  • David Nix David Nix committed [r253]

    Lots of modifications to the Telescriptor app

  • David Nix David Nix committed [r252]

    Telescriptor changes.

  • David Nix David Nix committed [r251]

    More static methods....

  • David Nix David Nix committed [r250]

    Fixed a warning message related to exon size, a...

  • David Nix David Nix committed [r249]

    Mods to support the Telescriptor....

  • David Nix David Nix committed [r248]

    New app and supporting classes for detailed Tel...

  • David Nix David Nix committed [r247]

    Added more output options for showing sample na...

  • David Nix David Nix committed [r246]

    Modified default bps to extract alignment count...

  • David Nix David Nix committed [r245]

    Added option to skip alt comparison when scorin...

  • David Nix David Nix committed [r243]

    AllelicExpressionDetector

  • David Nix David Nix committed [r59]

    Added mm10 genome build file and ensembl transc...

  • David Nix David Nix modified ticket #34

    SamAlignmentExtractor

  • David Nix David Nix committed [r238]

    Updated picard jars. They did a big package rea...

  • David Nix David Nix modified ticket #33

    DEseq filters for USeq 8.6.4 DRDS application

  • David Nix David Nix committed [r237]

    Modified RNASeq app to use DESeq2 for the scann...

  • David Nix David Nix committed [r236]

    Relaxed the thresholds for calling splice damag...

  • David Nix David Nix committed [r235]

    Brought the RNASeq, ChIPSeq, and MultipleReplic...

  • David Nix David Nix committed [r234]

    Switched the default behavior to merge stranded...

  • David Nix David Nix committed [r233]

    Cleaned up the code in the VCFComparator. Put ...

  • David Nix David Nix committed [r232]

    Lots of clean up.

  • David Nix David Nix committed [r20]

    Added classes and methods for creating and sear...

  • David Nix David Nix committed [r19]

    Added a goto URL method.

  • David Nix David Nix committed [r18]

    Added classes to generate IGVSession.xml files ...

  • David Nix David Nix committed [r17]

    Modified instructions to skew everything to tho...

  • David Nix David Nix committed [r229]

    Added enhancements to the diff splice detection...

  • David Nix David Nix committed [r15]

    Lots of mods to support coding, TSS, and termin...

  • David Nix David Nix committed [r13]

    Lots of reorganization in how the Genome and as...

  • David Nix David Nix committed [r12]

    Added benchmarking app to intersect mock chIPSe...

  • David Nix David Nix committed [r11]

    Added support for intersecting query regions wi...

  • David Nix David Nix committed [r10]

    Added GenomeTranscriptomeTestApp that loads an...

  • David Nix David Nix committed [r9]

    Added directory for annotation files and those ...

  • David Nix David Nix committed [r8]

    Lotta mods and renaming...

  • David Nix David Nix committed [r3]

    Testing commit on a file

  • David Nix David Nix committed [r2]

    Initial checkin!

  • David Nix David Nix committed [r1]

    Share project "BioMiner" into "https://svn.code...

  • David Nix David Nix committed [r227]

    BisStat

  • David Nix David Nix committed [r226]

    Mods to catch null data issues where no vcf rec...

  • David Nix David Nix committed [r225]

    VCFSpliceAnnotator

  • David Nix David Nix posted a comment on discussion Help

    Found a workaround, just modify the cigar string to indicate the alignment matches,...

  • David Nix David Nix posted a comment on discussion Open Discussion

    Is there any file format I could use to display single or better yet multiple amino...

  • David Nix David Nix committed [r220]

    Adding zscore support to the VCFSpliceAnnotator

  • David Nix David Nix committed [r219]

    SamTranscriptomeParser & DefinedRegionDifferent...

  • David Nix David Nix committed [r218]

    Minor mods to DRDS with option to exclude utr b...

  • David Nix David Nix committed [r217]

    Lots of mods, most are related to changing a me...

  • David Nix David Nix posted a comment on discussion Open Discussion

    Ahh, needed to modify the Makefile and point it to samtools. Now seeing this error:...

  • David Nix David Nix posted a comment on discussion Open Discussion

    Hello Folks, Looks like the binary is missing from your latest breakdancer-1.1.2...

  • David Nix David Nix posted a comment on discussion Help

    Is it possible to visualize soft masked bases from a bam file? By default these are...

  • David Nix David Nix committed [r207]

    Added latest apps.

  • David Nix David Nix committed [r206]

    Latest mods for associating variants with splic...

  • David Nix David Nix committed [r202]

    Mods to STP to output just spliced alignments.

  • David Nix David Nix committed [r200]

    Added indel support to the VCFSpliceAnnotator

  • David Nix David Nix committed [r199]

    * Added a catch to skip calculating stats on bi...

  • David Nix David Nix committed [r198]

    Added new SamSVFilter app to build

  • David Nix David Nix committed [r197]

  • David Nix David Nix committed [r196]

    Backed out Darrens changes until these are opti...

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