cistrome/MIRA

Issues

• Topic model fails with single job

  #46 opened 6 months ago by samzarr
  0

• NITE model prediction Error

  #45 opened 9 months ago by xgaoo
  0

• LinAlgError: Singular matrix for some of the data

  #42 opened 10 months ago by Yansr3
  4

• IndexError: Unknown indexer Ellipsis of type <class 'ellipsis'>

  #41 opened 9 months ago by WENHUAN22
  1

• OneHotEncoder: unexpected keyword argument

  #44 opened 9 months ago by xgaoo
  1

• The least populated class in y has only 1 member, which is too few. The minimum number of groups for any class cannot be less than 2.

  #36 opened a year ago by christophechu
  5

• API on website not showing up

  #43 opened 9 months ago by justinejacobi
  2

• Issue running mira.tl.get_motif_hits_in_peaks

  #39 opened 9 months ago by jmmuncie
  4

• PicklingError: Could not pickle the task to send it to the workers.

  #32 opened 10 months ago by Yansr3
  1

• BayesianTuner error

  #40 opened a year ago by WENHUAN22
  1

• NITE model prediction expected scalar type Double but found Float

  #34 opened a year ago by Yansr3
  3

• Using Alternative Preprocess Methods for Training RP Models

  #38 opened a year ago by shycheng
  3

• ValueError: Tried to step 7921 times. The specified number of total steps is 7920

  #37 opened a year ago by ChloeHJ
  4

• accessibility model input data must be integers

  #33 opened a year ago by yuyanMaggieliu
  1

• gradient tuner overflow

  #31 opened a year ago by Yansr3
  4

• BayesianTuner Assertion Error

  #35 opened a year ago by dfdeascanis
  2

• Question about installation

  #28 opened a year ago by Yansr3
  12

• Question about BayesianTuner

  #30 opened a year ago by MoLuLuMo
  5

• Question for ATAC topic model

  #29 opened a year ago by MoLuLuMo
  4

• Input data must be raw transcript counts, represented as integers. Provided data contains non-integer values.

  #24 opened a year ago by samhkim
  5

• speed

  #27 opened a year ago by bjstewart1
  0

• questions for batch effect

  #23 opened 2 years ago by rdf1993
  7

• IndexError in mira.pl.plot_stream

  #26 opened a year ago by jmmuncie
  1

• Is MIRA being actively developed / maintained

  #25 opened 2 years ago by akundaje
  2

• Repeat individual tuning trials that terminate with errors?

  #22 opened 2 years ago by jmmuncie
  2

• Finding reconstructed gene by cell from different models

  #12 opened 2 years ago by Connorr0
  6

• suggested upsteam processing before mira

  #20 opened 2 years ago by KailiBio
  2

• Question on transfer learning

  #15 opened 2 years ago by tinakeshav
  1

• "mira.tl.get_motif_hits_in_peaks" results in bin/sh 1:moods-dna.py not found when in environment

  #17 opened 2 years ago by Chadmiumoxid
  2

• MIRA code ocean capsule inaccessible

  #18 opened 2 years ago by nandankita
  1

• Question for multiple datasets

  #19 opened 2 years ago by jjacobi3
  5

• Error running get_learning_rate_bounds() for an Accessibility Topic Model

  #21 opened 2 years ago by jmmuncie
  1

• model.get_enriched_TFs returns no TFs for any topics despite motif hits in scanning

  #16 opened 2 years ago by alonmillet
  1

• Joint representation UMAP not appearing as in walkthrough (with supplied data)

  #13 opened 2 years ago by Connorr0
  3

• How can peaks associated with a given gene be extracted?

  #10 opened 3 years ago by shaistamadad
  5

• What is the best way to decide whether a gene is NITE or LITE regulated?

  #11 opened 3 years ago by shaistamadad
  1

• AssertionError: Graphs with multiple connected components may not be used. Subset cells to include only one connected component.

  #9 opened 3 years ago by shaistamadad
  1

• IndexError: index 39840 is out of bounds for axis 0 with size 20479

  #8 opened 3 years ago by shaistamadad
  2

• canonical TSS site data for training the LITE Model

  #7 opened 3 years ago by shaistamadad
  2

• Errors when loading trained models

  #6 opened 3 years ago by KongMingxi
  4

• Exception: Error while scanning for motifs: /bin/sh: 1: moods-dna.py: not found

  #4 opened 3 years ago by shaistamadad
  8

• mira.tl.get_distance_to_TSS(): human genome equivalent for parameter : genome_file

  #5 opened 3 years ago by shaistamadad
  2

• Zero motif hits when using human FA

  #3 opened 3 years ago by Chengwei94
  4

• rna_topic_pathways(7, 500, 5, 1, True) TypeError: __init__() got an unexpected keyword argument 'location'

  #2 opened 3 years ago by shijianasdf
  3

• Hyperparameter tuning is too slow

  #1 opened 3 years ago by longfeili5170
  6