calico/basenji

Issues

• akita train error

  #200 opened 4 months ago by guandailu
  0

• Question of expected data

  #198 opened 6 months ago by seraphimangel77
  1

• AssertionError, Basenji_test.py 'Conv1D' object has no attribute 'input_shape'

  #199 opened 6 months ago by PouriaAzadehR
  1

• Basenji installation issues

  #194 opened 6 months ago by seraphimangel77
  4

• Error from basenji import genome

  #197 opened 6 months ago by seraphimangel77
  1

• basenji_read overflow

  #196 opened 6 months ago by ElArquitectorgo
  1

• Question about the preprocessing script bam_cov.py

  #195 opened 6 months ago by whui2bioinformatics
  1

• Prepare data

  #191 opened 7 months ago by amingc3
  1

• tutorial training with --sample 0.05

  #182 opened a year ago by zyj1729
  3

• Problems during model training.

  #192 opened 8 months ago by amingc3
  7

• Tensorflow / Traceback error.

  #193 opened 7 months ago by jesspeers
  2

• Reproduce the Enformer's input sequences split

  #190 opened 9 months ago by sararb
  1

• OOM issue

  #189 opened 10 months ago by BioCUCKOO
  0

• Issue with final matrix?

  #188 opened 10 months ago by 16nbb1
  0

• When using Akita for single-cell prediction on the HCT116 cell line, the Pearson correlation coefficient is much lower.

  #186 opened a year ago by 1944498970
  8

• Akita: Loading weights for newer models results in mismatch

  #187 opened a year ago by jakevc
  2

• Attention layer

  #184 opened a year ago by samuel-g-bates
  4

• Seeking Guidance on bam_cov.py Parameters

  #185 opened a year ago by zhanxiangzong
  2

• Pre-process tutorial file not working

  #181 opened a year ago by riapai
  2

• Making Akita predictions for different bin size

  #183 opened a year ago by shu-z
  2

• How to convert the keras model to a basenji model

  #180 opened a year ago by houruiyan
  1

• How to set different GPU No. ?

  #178 opened a year ago by houruiyan
  2

• Stable environment configuration

  #179 opened a year ago by tzhu-bio
  1

• basenji_data_align.py train/test/validation splits

  #177 opened a year ago by maroll
  2

• handling blacklist\unmappable

  #176 opened a year ago by yardenmatok203
  1

• Black list

  #174 opened a year ago by yardenmatok203
  6

• Expose 'raw' as an argument?

  #173 opened a year ago by Yaoyx
  2

• None in maps

  #171 opened a year ago by yardenmatok203
  4

• .hic

  #172 opened a year ago by yardenmatok203
  0

• Problem with calculating the target based on the gene sequence

  #170 opened a year ago by wananal
  1

• No checkpoints found.

  #169 opened a year ago by houruiyan
  1

• distiller

  #168 opened a year ago by yardenmatok203
  6

• Weird targets

  #167 opened a year ago by yardenmatok203
  2

• error with akita_data. py

  #165 opened a year ago by yardenmatok203
  3

• Output regions from Akita

  #166 opened a year ago by ahmedabbas811
  1

• Question about Basenji2 receptive field

  #163 opened a year ago by pkathail
  2

• How to prepare TFRecords files for saluki training

  #164 opened a year ago by hamanakakohei
  1

• pygene installation

  #162 opened 2 years ago by hamanakakohei
  2

• Question about Gene Expression Training Preprocessing

  #161 opened 2 years ago by wkl1990
  3

• akita can't train

  #160 opened 2 years ago by bioczsun
  1

• Training with multiple directories

  #157 opened 2 years ago by raphaelmourad
  1

• Problem with multigenome training with > 2 genomes

  #158 opened 2 years ago by raphaelmourad
  1

• Tensorflow records generated with basenji_data.py differ from original

  #159 opened 2 years ago by icdh99
  1

• question about clip threshold in basenji/enformer.

  #156 opened 2 years ago by r1cheu
  2

• Basenji Features used for Whole Blood Fine-Mapping

  #153 opened 2 years ago by aga-relation
  3

• Blacklist file & unmappable regions

  #155 opened 2 years ago by icdh99
  2

• failed running "basenji_sat_bed.py" in tutorials

  #152 opened 2 years ago by yal054
  4

• Issue running basenji_data.py

  #154 opened 2 years ago by petnas
  2

• train/test/valid sequences for predetermined regions

  #151 opened 2 years ago by icdh99
  2

• fasta file of saluki_predict_fasta.py

  #150 opened 2 years ago by Jojo-LIU-LIU
  1