loosolab/TF-COMB

Issues

• DiffCombObj().plot_heatmap does not pass kwargs to tfcomb.plotting.heatmap

  #84 opened 4 months ago by rwiegan
  0

• import graphviz

  #83 opened 7 months ago by pavelToman
  0

• Please kindly explain this figure

  #74 opened 10 months ago by Rajashree93
  3

• What does co-occurrence mean based on cosine and z-scores?

  #76 opened a year ago by Rajashree93
  2

• Unexpected keyword argument 'max_distance'

  #80 opened a year ago by ancient-learner
  1

• Error at market_basket step

  #77 opened a year ago by ancient-learner
  2

• `TFBSpairList.pairMap` function chromosome naming issue

  #75 opened a year ago by Myrtle-bio
  1

• Installation using pip install .

  #70 opened a year ago by ybaeus
  2

• Details about subsetting TF-TF co-occurring pairs

  #72 opened a year ago by Myrtle-bio
  2

• No image output on remote sever.

  #60 opened a year ago by Rajashree93
  3

• Plot footprints

  #66 opened a year ago by Rajashree93
  2

• Annotations

  #65 opened a year ago by Rajashree93
  3

• Annotation

  #63 opened a year ago by Rajashree93
  2

• Z score

  #67 opened a year ago by Rajashree93
  7

• FloatingPointError in select_significant_rules()

  #73 opened a year ago by Myrtle-bio
  1

• For CUT&RUN data

  #68 opened a year ago by ybaeus
  9

• Kernal crashing at get_pair_locations

  #69 opened a year ago by annrosebright
  3

• AttributeError: 'OneMotif' object has no attribute 'get_pssmm'

  #62 opened 2 years ago by VenkateshLab
  5

• Meme_Format Motif Input

  #64 opened 2 years ago by KaltenbacherT
  2

• Issue while installing TF-comb

  #61 opened 2 years ago by VenkateshLab
  4

• TFcomb changes numpy error handling

  #55 opened 2 years ago by hschult
  4

• Interpreting the biological context of PairMap, PairTrack, PairTrackAnimation and PairLines

  #58 opened 2 years ago by archieandrews10
  1

• Unable to see gene_id column in annotated output

  #50 opened 2 years ago by archieandrews10
  4

• Unable to plot distances for stranded TFBS

  #54 opened 2 years ago by msbentsen
  1

• Kde plot not working [distObj]

  #57 opened 2 years ago by vheger
  0

• Adjust verbosity of external modules

  #53 opened 2 years ago by hschult
  0

• InputError: Region is out of bounds in the given genome

  #49 opened 2 years ago by GudaLab
  2

• AttributeError: module 'matplotlib' has no attribute '_version_'

  #47 opened 2 years ago by hcph
  3

• How to get all TF-TF pairs' location

  #48 opened 2 years ago by hcph
  2

• No releases yet?

  #46 opened 2 years ago by sassy-crick
  3

• not possible to change distribution threshold in DiffCombObj.select_rules()

  #31 opened 3 years ago by vheger
  1

• motif position line not displayed correctly in TFBSPairList.pairMap()

  #42 opened 3 years ago by vheger
  4

• median produces error in analyse_distances

  #34 opened 3 years ago by vheger
  2

• UnpicklingError for loading of CombObj

  #39 opened 3 years ago by oKoch
  2

• Floating Point Error in

  #37 opened 3 years ago by oKoch
  2

• Some documentation markup is messed up (only distObj)

  #25 opened 3 years ago by vheger
  0

• Subselection with a TF that does not exist returns no Message/Error

  #33 opened 3 years ago by oKoch
  1

• linear regression is slow for big datasets

  #21 opened 3 years ago by vheger
  0

• plot negative column correct

  #16 opened 3 years ago by vheger
  1

• add possibility to trigger analyze distances() from within DiffComb

  #32 opened 3 years ago by vheger
  0

• Floating point error by differential analyses of sub-selection

  #23 opened 3 years ago by oKoch
  4

• Split of dependencies for TF-COMB and documentation

  #28 opened 3 years ago by msbentsen
  2

• resolve_overlapping in .TFBS_from_motifs() is super slow

  #19 opened 3 years ago by msbentsen
  1

• Update Documentation for function in tfcomb/utils.py get_pair_locations()

  #24 opened 3 years ago by oKoch
  6

• implement rank score

  #20 opened 3 years ago by vheger
  0

• Function needed: integrate_external_data()

  #18 opened 3 years ago by msbentsen
  1

• add raw count column

  #17 opened 3 years ago by vheger
  0

• example notebook for distance analysis

  #14 opened 3 years ago by vheger
  0

• Shift signal is too slow

  #15 opened 3 years ago by vheger
  1

• implement overlapping handling count_distances

  #12 opened 3 years ago by vheger
  0