andersen-lab/Freyja

Issues

• Inconsistent curated lineages naming

  #246 opened 3 months ago by gyebra-phs
  3

• SARS-CoV-2 barcodes update 2024-08

  #247 opened 3 months ago by ktmeaton
  3

• pyarrow missing from conda environment in v1.5.1

  #244 opened 4 months ago by ktmeaton
  3

• ECOS deprecation and increasing frequency of demix errors

  #238 opened 4 months ago by ktmeaton
  3

• Breaking out novel variants given BA.2.86 evolution

  #241 opened 4 months ago by andrew-rothstein
  3

• Freyja plot key is hard to read

  #234 opened 4 months ago by nicolegobo
  3

• Using --depthcutoff for some recent high coverage genomes

  #237 opened 4 months ago by owenssm
  1

• Wrong lineages?

  #197 opened 4 months ago by LauraVP1994
  1

• clarification about the result

  #221 opened 4 months ago by Petrichor-sudo
  4

• Freyja covariants runtime error

  #226 opened 5 months ago by RainerWaldmann
  2

• Freyja plot help

  #196 opened 8 months ago by ADY-PANDA
  8

• [BUG]: barcode version is stuck on 04_30_2024-01-10

  #236 opened 5 months ago by erinyoung
  3

• Freyja plot explanation

  #235 opened 6 months ago by ChromatinLab
  2

• Freyja plot error

  #228 opened 6 months ago by ChromatinLab
  5

• Random seed for freyja boot for consistent results

  #229 opened 6 months ago by ktmeaton
  1

• [BUG] Unexpected Behavior Depending on Reference

  #233 opened 6 months ago by whottel
  2

• [BUG] freyja exits rather than raising errors

  #227 opened 6 months ago by wutron
  1

• Lineage specific plot trouble shooting

  #220 opened 8 months ago by Aishah86
  3

• Reduce runtime

  #184 opened 7 months ago by erinyoung
  2

• cvxpy.error.SolverError: Solver 'ECOS' failed

  #217 opened 7 months ago by EricFournier3
  10

• -like lineages grouped within "Other" VOC

  #213 opened 7 months ago by ktmeaton
  4

• Some problem about the UshER barcodes output

  #210 opened 7 months ago by Bin-Ma
  1

• The purpose of providing reference genomes file, and Demixing error

  #216 opened 8 months ago by Petrichor-sudo
  1

• AttributeError: 'Series' object has no attribute 'columns'

  #215 opened 8 months ago by jchorl
  0

• Improve documentation with default values used

  #211 opened 8 months ago by tavareshugo
  1

• Clarify difference between `--covcut` and `--depthcutoff`

  #212 opened 8 months ago by tavareshugo
  2

• freyja demix error citing insufficient sequencing depth

  #208 opened 8 months ago by michellescribner
  3

• freyja boot error messages missing in output

  #206 opened 9 months ago by ktmeaton
  2

• Custom summarised lineage demix option?

  #193 opened 9 months ago by AliceMichie93
  2

• Freyja plot failures with low-coverage samples

  #203 opened 9 months ago by kevinlibuit
  2

• ECOS problem reopening not due to low sample coverage but update

  #201 opened 9 months ago by CeliaRodrigues
  12

• Manual install

  #189 opened 10 months ago by LauraVP1994
  1

• Spike coverage estimates

  #202 opened 9 months ago by joshuailevy
  0

• Is there a risk that freyja recover the wrong XDD relative lineage abundances?

  #205 opened 9 months ago by Fuyulinn
  2

• Requesting help with understanding and usage of `--confirmedonly` flag

  #200 opened 9 months ago by NickD-BHSc
  2

• Add option to retain intermediate figure outputs

  #195 opened 9 months ago by jchorl
  4

• raise TypeError(f"{cls.__name__}.name must be a hashable type")

  #188 opened 9 months ago by bsalehe
  1

• freyja plot --lineages

  #186 opened 9 months ago by mikal16
  2

• Minimum Depth Question

  #194 opened 9 months ago by whottel
  3

• No group keys passed!

  #187 opened a year ago by LauraVP1994
  6

• RA not summing to 1

  #190 opened a year ago by djfeistel
  5

• Freyja dash: KeyError and ValueError

  #183 opened a year ago by bsalehe
  2

• key error for EG.5.1.8

  #180 opened a year ago by xsitarcik
  8

• Pandas update breaks demixing

  #179 opened a year ago by gabimuir
  2

• Potential bug in sorting code for covariants function

  #181 opened a year ago by JHarrisonEcoEvo
  1

• how to update freyja from 1.3 to 1.4.5

  #175 opened a year ago by ybdong919
  2

• Error running "freyja update"

  #178 opened a year ago by susancollins
  3

• Abundance 100%

  #177 opened a year ago by Linnet111
  3

• freyja covariants KeyError

  #172 opened a year ago by djfeistel
  4

• lineage Misc?

  #171 opened a year ago by ybdong919
  5