Issues

• Many scripts use "dumb" relative paths.

  koadman/proxigenomics#50 · Filter by author cerebis opened on Dec 1, 2015

• external binaries using path relative to invocation directory

  koadman/proxigenomics#49 · Filter by author cerebis opened on Dec 1, 2015
  1

• Simulation pipeline requires an overarching point of entry

  koadman/proxigenomics#47 · Filter by author cerebis opened on Nov 13, 2015
  1

• External dependencies and overall structure a mess.

  koadman/proxigenomics#45 · Filter by author cerebis opened on Nov 9, 2015

• Permutation control split over both file existence and parameter settings

  koadman/proxigenomics#44 · Filter by author cerebis opened on Nov 9, 2015

• bam2edges and edges2metis should be combined.

  koadman/proxigenomics#43 · Filter by author cerebis opened on Oct 28, 2015

• Ideally, our generated internal files should have annotation fields.

  koadman/proxigenomics#40 · Filter by author cerebis opened on Oct 27, 2015
  1

• bcubed.py does not notice when supplied the wrong file format.

  koadman/proxigenomics#39 · Filter by author cerebis opened on Oct 27, 2015

• add support for running pipeline outside $HOME

  koadman/proxigenomics#38 · Filter by author koadman opened on Oct 16, 2015

• binaries required by mktree.sh are unavailable

  koadman/proxigenomics#37 · Filter by author koadman opened on Oct 16, 2015
  2

• Support both Hi-C and meta3C read simulation

  koadman/proxigenomics#36 · Filter by author cerebis opened on Sep 8, 2015

• Large files and method of parsing BAM

  koadman/proxigenomics#35 · Filter by author cerebis opened on Jul 30, 2015
  2

• contact_map.py memory usage

  koadman/proxigenomics#34 · Filter by author koadman opened on Jul 13, 2015
  10

• weighted extended bcubed precision and recall

  koadman/proxigenomics#33 · Filter by author cerebis opened on Mar 25, 2015
  3

• Pipeline path references require refactoring

  koadman/proxigenomics#20 · Filter by author cerebis opened on Feb 3, 2015

• Make pipeline runtime environment agnostic.

  koadman/proxigenomics#18 · Filter by author cerebis opened on Feb 2, 2015
  2

• Symmetric measures can be used as consensus tests

  Clusteringenhancement
  koadman/proxigenomics#14 · Filter by author cerebis opened on Apr 1, 2014 · Analysis framework and experiment

• Soft-clustering descriptive values

  Clusteringenhancement
  koadman/proxigenomics#13 · Filter by author cerebis opened on Apr 1, 2014 · Validated soft clustering and scoring

• Some code is running on the head node

  bug
  koadman/proxigenomics#12 · Filter by author cerebis opened on Mar 31, 2014 · Analysis framework and experiment

• Soft-clustering

  Clusteringenhancement
  koadman/proxigenomics#10 · Filter by author cerebis opened on Mar 18, 2014 · Validated soft clustering and scoring
  1

• Ground truth is only a guess

  Clusteringenhancement
  koadman/proxigenomics#9 · Filter by author cerebis opened on Mar 18, 2014 · Analysis framework and experiment

• Should performance metrics consider only classification

  Clusteringenhancement
  koadman/proxigenomics#8 · Filter by author cerebis opened on Mar 18, 2014 · Analysis framework and experiment

• Edge weighting

  Clusteringenhancement
  koadman/proxigenomics#7 · Filter by author cerebis opened on Mar 18, 2014 · Analysis framework and experiment

• Pruning of input graph

  Clusteringenhancement
  koadman/proxigenomics#6 · Filter by author cerebis opened on Mar 18, 2014 · Analysis framework and experiment

• Community profile by specifying distribution function

  community definitionenhancement
  koadman/proxigenomics#2 · Filter by author cerebis opened on Mar 11, 2014 · Support for variable abundance in WGS data.
  1