baliga-lab/cmonkey2

Issues

• conda install?

  #81 opened 8 months ago by ruthangelina
  0

• Wondering if Cmonkey2 works well with scRNAseq dataset

  #79 opened a year ago by Rohit-Satyam
  1

• local rsat files can't be read correctly

  #80 opened a year ago by hughit32
  2

• error when using example data

  #78 opened 3 years ago by tangbozeng
  0

• Error

  #77 opened 4 years ago by vpandey-om
  7

• checkratios flag fails

  #60 opened 5 years ago by adelomana
  0

• Operational Error

  #76 opened 6 years ago by as1403
  3

• python 3 cmonkey crashing early

  #74 opened 7 years ago by fwschmitz
  5

• A question regarding RSAT

  #63 opened 7 years ago by ABanaeiEsfahani
  17

• Problem with Aspergillus

  #49 opened 7 years ago by IvanV87
  2

• Cannot display clusters where all genes are included

  #43 opened 7 years ago by sdanzige
  0

• Errors in attempted mouse and human runs

  #47 opened 7 years ago by vectorborne5
  6

• cm2view: cluster list initially always shows iteration 1

  #67 opened 7 years ago by weiju
  1

• cmonkey crashes with yeast

  #69 opened 7 years ago by kieran-mace
  2

• KeyError running human data

  #75 opened 7 years ago by LuziaThea
  1

• error when using example data

  #73 opened 7 years ago by wwick
  5

• Options for running cMonkey2 with an organism that is not included in the KEGG database

  #70 opened 7 years ago by vvelasqz
  1

• Minor bug in stringdb.py

  #71 opened 7 years ago by izzi-13
  2

• Invalid literal error running human data

  #68 opened 8 years ago by maxneal
  0

• cmonkey2 does not work with meme 4.11

  #51 opened 8 years ago by NelleV
  2

• Python 2.7.x/pip Installation issue (was: I can't load.)

  #56 opened 8 years ago by jacobvalenzuela
  5

• HTTP error

  #66 opened 8 years ago by prashantkum7
  8

• MAST error in attempted human run

  #54 opened 8 years ago by cfbuenabadn
  3

• To know the scores

  #65 opened 8 years ago by ABanaeiEsfahani
  2

• add gene annotations: RSAT gene

  #64 opened 8 years ago by weiju
  0

• urllib2.HTTPError: HTTP Error 404: Not Found

  #62 opened 8 years ago by ABanaeiEsfahani
  3

• Split out example_data and testdata from code repo

  #40 opened 8 years ago by dreiss-isb
  1

• 0 edges in network 'operon' error for Halobacterium test run

  #61 opened 8 years ago by maxneal
  5

• --use_BSCM is not working on my datset

  #53 opened 8 years ago by ABanaeiEsfahani
  5

• installation crashes in osiris

  #59 opened 8 years ago by adelomana
  1

• MEME parallel environment fail

  #58 opened 8 years ago by adelomana
  4

• problem with STRING file

  #57 opened 8 years ago by adelomana
  5

• executable paths

  #55 opened 8 years ago by adelomana
  2

• Crashes if --num_iterations 2

  #42 opened 9 years ago by sdanzige
  1

• Python 3

  #50 opened 9 years ago by mruffalo
  3

• motif_info_id in 'meme_motif_sites' == ROWID in motif_infos?

  #38 opened 10 years ago by scalefreegan
  2

• Can't map meme motifs to gene names in output sqlite db

  #37 opened 10 years ago by scalefreegan
  0

• store all iterations (or every 10) in iteration_stats?

  #36 opened 10 years ago by dreiss-isb
  1

• xmlrunner requirement?

  #35 opened 10 years ago by scalefreegan
  1

• Add port selector for cmviewer

  #33 opened 10 years ago by JohnCEarls
  0

• viewer defaults and requests

  #27 opened 11 years ago by dreiss-isb
  10

• meme still required if --nomotifs is turned on

  #28 opened 11 years ago by dreiss-isb
  1

• running with --nomotifs should skip MEME step altogether (for speed)

  #29 opened 11 years ago by dreiss-isb
  2

• output directory still not working right

  #24 opened 11 years ago by dreiss-isb
  0

• MEME versions: selection/detection/dependency update

  #15 opened 11 years ago by justinashworth
  1

• Current version of BeautifulSoup

  #18 opened 12 years ago
  4

• JSON and R

  #14 opened 12 years ago by fschmitz
  1

• None value returns from meme / mast

  #12 opened 13 years ago by fschmitz
  2

• logging

  #11 opened 13 years ago by fschmitz
  11

• logging module usage (and IPython)

  #9 opened 13 years ago by justinashworth
  2