qiime2/q2-feature-classifier

Issues

• investigate alternative serialization format for classifiers to improve security

  #202 opened 5 months ago by gregcaporaso
  0

• Test suite does not build with scikit-learn 1.2.1

  #187 opened 6 months ago by tillea
  2

• Using new NCBI 4 experimental taxonomic nt databases for qiime2 classifer

  #200 opened 6 months ago by jibrantahir
  1

• Find Consensus Annotation Parallelization

  #198 opened 7 months ago by Alexander-Jorjorian
  0

• Higher RAM use in classify-consensus-vsearch version 2022.8+

  #188 opened 10 months ago by nbokulich
  1

• pop from empty list error when taxonomy label not complete

  #93 opened 7 years ago by BenKaehler
  12

• DNNs for feature classification

  #129 opened a year ago by mortonjt
  6

• Read orientation auto detection failure

  #177 opened 3 years ago by wasade
  6

• Warn when read orientation autodetect flips orientation?

  #103 opened a year ago by BenKaehler
  1

• Make API consistent for classifiers?

  #72 opened a year ago by johnchase
  1

• ENH: use metadata to input class priors

  #76 opened a year ago by BenKaehler
  2

• Copy number prediction

  #108 opened a year ago by mortonjt
  4

• failure on empty input sequence file

  #193 opened a year ago by nick-youngblut
  3

• Unpin SKL (0.23.1)

  #166 opened a year ago by thermokarst
  0

• Wrap makeblastdb to generate indexed blast database

  #158 opened a year ago by nbokulich
  2

• Utilize one database instance for multiple classification jobs

  #190 opened a year ago by valentynbez
  0

• fit-classifier-sklearn

  #186 opened 2 years ago by scmicrosys
  0

• `classify-consensus-*`: output alignment results report?

  #152 opened 2 years ago by nbokulich
  0

• BUG: _autotune_reads_per_batch fails when input is empty

  #175 opened 3 years ago by nbokulich
  0

• Testing classifier issue - Parameter 'confidence' received -1 as an argument, which is incompatible with parameter type: Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable')

  #174 opened 3 years ago by XrandallX
  1

• --p-reads-per-batch should be made consistent with --p-confidence

  #167 opened 4 years ago by BenKaehler
  0

• pop from empty list error when taxonomy label not complete

  #168 opened 4 years ago by ssavvi
  1

• TODO: Train new feature-classifiers using scikit-learn 0.23.1

  #161 opened 4 years ago by thermokarst
  3

• `classify-sklearn` orientation detector will raise confidence error

  #159 opened 5 years ago by nbokulich
  0

• No way to figure out read orientation used after executing an action

  #88 opened 7 years ago by ElDeveloper
  5

• `extract-reads`: clarify primer orientation in help documentation

  #121 opened 4 years ago by nbokulich
  0

• extract-reads: add trim-right option

  #160 opened 4 years ago by nbokulich
  2

• `classify-sklearn`: MemoryError should be more user-friendly

  #131 opened 4 years ago by nbokulich
  6

• classify-consensus-blast: expose num_threads

  #155 opened 5 years ago by nbokulich
  9

• classify-consensus-vsearch: expose maxhits option (and other options)

  #151 opened 5 years ago by nbokulich
  3

• `extract-reads`: add read orientation parameter

  #124 opened 5 years ago by nbokulich
  11

• `extract-reads`: validate trimming parameters prior to extraction

  #119 opened 5 years ago by nbokulich
  2

• `extract-reads`: add n-jobs parameter

  #135 opened 5 years ago by ebolyen
  2

• Fix warnings in unit tests

  #142 opened 5 years ago by BenKaehler
  2

• joblib now a dependency in scikit-learn

  #134 opened 5 years ago by ChrisKeefe
  2

• Turn down the default for --p-reads-per-batch

  #130 opened 6 years ago by BenKaehler
  3

• `classify-consensus-blast` should have a cutoff for query coverage

  #100 opened 6 years ago by nbokulich
  1

• `extract-reads` should have a min/max length parameters

  #110 opened 6 years ago by nbokulich
  1

• `classify-consensus-vsearch`: allow maxaccepts=0

  #114 opened 6 years ago by nbokulich
  0

• `classify-consensus-*` methods: improve maxaccepts param description

  #112 opened 6 years ago by nbokulich
  0

• New "memory" parameter sneaking through from sklearn to user interface

  #101 opened 6 years ago by BenKaehler
  2

• set defaults to the balanced parameters from the paper

  #104 opened 6 years ago by BenKaehler
  0

• Should classify-sklearn error when "dummy" jobs are created?

  #90 opened 7 years ago by ElDeveloper
  5

• benchmark `classify-sklearn` parallelization

  #97 opened 7 years ago by nbokulich
  1

• Missing parameter descriptions in classify-sklearn

  #85 opened 7 years ago by ElDeveloper
  3

• Why is classify-consensus-vsearch so slow?

  #80 opened 7 years ago by BenKaehler
  4

• ChunkedHashingVectorizer is not compatible with sklearn 0.19.0

  #84 opened 7 years ago by ebolyen
  2

• Detach `num_threads` from blast parameter list

  #77 opened 7 years ago by jakereps
  0

• fit-classifier-naive-bayes raises a ValueError for valid input

  #74 opened 7 years ago by BenKaehler
  0

• unassigned sequences

  #67 opened 7 years ago by BenKaehler
  1