Genentech/gReLU

Issues

• Questions about early stopping

  #84 opened 2 months ago by HelloWorldLTY
  0

• wrong input file pointed by the tutorial 3_train.ipynb

  #24 opened 2 months ago by mhfzsharmin
  4

• Training multitask model

  #82 opened 2 months ago by nkempynck
  2

• Incompatibility between modisco with ISM and Specificify transform with subtract function

  #80 opened 2 months ago by dagarfield
  1

• Update tangermeme backend

  #55 opened 2 months ago by avantikalal
  0

• Automatically catch intervals which extend beyond the chr?

  #54 opened 3 months ago by cafletezbrant
  1

• Add axis option to poissonmultinomial loss

  #68 opened 2 months ago by avantikalal
  0

• Consider strand column in `merge_intervals`

  #63 opened 2 months ago by avantikalal
  0

• Support fast attention

  #64 opened 3 months ago by avantikalal
  1

• Questions about the acceptable sequence length of borzoi

  #72 opened 3 months ago by HelloWorldLTY
  3

• Loading custom models

  #76 opened 3 months ago by saninta0212
  1

• Can't view available models

  #46 opened 3 months ago by Al-Murphy
  2

• Fix annotation direction in plot_tracks

  #61 opened 3 months ago by avantikalal
  0

• Update motifs in resources

  #70 opened 3 months ago by avantikalal
  0

• Support indels

  #65 opened 3 months ago by avantikalal
  0

• Update doc string and input allowances for grelu.sequence.utils.resize

  #34 opened 5 months ago by dagarfield
  0

• Making train_params and model_params functional to add documentation and avoid duplication

  #38 opened 5 months ago by gokceneraslan
  6

• Enable deepshap for enformer models

  #56 opened 3 months ago by avantikalal
  0

• Save gReLU version in checkpoints

  #57 opened 3 months ago by avantikalal
  0

• Remove pretrainedmodel classes

  #58 opened 3 months ago by avantikalal
  0

• Check chromosomes when fine tuning?

  #59 opened 3 months ago by avantikalal
  0

• Add attribution score for motif hits

  #60 opened 3 months ago by avantikalal
  0

• Add a function to plot motif logos

  #62 opened 3 months ago by avantikalal
  0

• How to change the location of genome downloading path?

  #52 opened 3 months ago by HelloWorldLTY
  0

• Plans for on disk dataloaders?

  #40 opened 3 months ago by mtvector
  3

• guidelines to implement custom models

  #47 opened 4 months ago by MiqG
  1

• Questions about extracting variants with grelu

  #48 opened 3 months ago by HelloWorldLTY
  5

• Questions about reading variants

  #45 opened 4 months ago by HelloWorldLTY
  3

• filter_blacklist doesn't support obtaining custom blacklist from custom genome

  #9 opened 5 months ago by varsh7777
  2

• 'SparseCSCView' object has no attribute 'A'

  #23 opened 5 months ago by mhfzsharmin
  4

• Bugs in `PoissonMultinomialLoss` class

  #31 opened 5 months ago by MuhammedHasan
  1

• `PearsonCorrCoef` not reset correctly

  #27 opened 5 months ago by suragnair
  0

• Ref and alt reversed in VEP tutorial

  #33 opened 5 months ago by dagarfield
  0

• Loading models from the checkpoint leads to package version conflicts

  #28 opened 6 months ago by MuhammedHasan
  0

• Unexpected device for model. embed_on_dataset

  #19 opened 6 months ago by dagarfield
  3

• get_artifact() project not found error from

  #16 opened 6 months ago by colinshew
  0

• accessing genomes using genomepy

  #22 opened 6 months ago by mhfzsharmin
  2

• Training with `poisson_multinomial` + label preprocessing

  #17 opened 6 months ago by fteufel
  0

• Issues import bpnet negatives

  #12 opened 6 months ago by Jome0169
  4

• pyGenomeViz 1.0 broke API

  #10 opened 6 months ago by gokceneraslan
  0