labgem/PPanGGOLiN

Issues

• 'ascii' codec

  #252 opened 2 months ago by yl030
  1

• Annotation error: gene coordinates exceeding contig length

  #254 opened a month ago by MilanAdd
  2

• ValueError: max() iterable argument is empty

  #264 opened a month ago by frdel1
  5

• ValueError: The gene family has not beed associated to a partition.

  #262 opened a month ago by frdel1
  7

• Non-deterministic clustering (possibly due to multi-threading)

  #263 opened a month ago by ktmeaton
  2

• conda installs old version

  #260 opened a month ago by IsabelFE
  2

• ppanggolin msa --partition core

  #231 opened 2 months ago by lfdelzam
  6

• rarefaction curve : Population must be a sequence

  #253 opened 2 months ago by emorinrae
  3

• Add gene name info in the Tile Plot

  #251 opened 2 months ago by JeanMainguy
  1

• RGP borders not in regions_of_plasticity.tsv

  #218 opened 2 months ago by KerrinSteensen
  4

• ppanggolin projection: ValueError: The region is already with a different spot.

  #243 opened 2 months ago by frdel1
  2

• Getting MSAs for single-copy gene families when duplicates are tolerated

  #223 opened 2 months ago by szhan
  3

• MAFFT error when running ppanggolin MSA

  #210 opened 2 months ago by jvfe
  9

• Reading the gbff file error

  #226 opened 2 months ago by seajane
  4

• Clarification about the contents of `gene_to_gene_family.tsv ` from projection

  #221 opened 2 months ago by szhan
  5

• Exception: Reading the gbff file. Expected type is string, given type was '<class 'NoneType'>'

  #203 opened 2 months ago by frdel1
  2

• different results ppanggolin projection with gbff or fasta files

  #207 opened 2 months ago by frdel1
  2

• RGP drawn in spot figure is incorrect

  #124 opened 2 months ago by Quentinfdg
  3

• Discrepancy between # of genes in RGPs?

  #122 opened 2 months ago by cizydorczyk
  2

• Rarefaction

  #195 opened 6 months ago by eduardags12
  9

• Gene family count matrix related with representative gene family .

  #217 opened 3 months ago by aababc1
  4

• Annotation with user-provided CDS fasta sequences

  #197 opened 3 months ago by seajane
  4

• Wrong File Type Error

  #185 opened 3 months ago by jacordova
  1

• error while writing genome annotations

  #233 opened 3 months ago by sulmanm1
  1

• Writing gene-related data failed

  #232 opened 3 months ago by dmartimarti
  3

• Written error core families sequences

  #179 opened 7 months ago by clelauden
  1

• product_string

  #222 opened 4 months ago by oclaisse
  2

• Error in ppanggolin msa when running all partitions

  #198 opened 6 months ago by ktmeaton
  3

• Does PPanGGOLiN provides functional annotation?

  #194 opened 6 months ago by cmonat
  3

• Gbk files

  #128 opened a year ago by Bury-Mone
  4

• Extract fasta files

  #191 opened 6 months ago by SamVaGo
  4

• Dead link

  #189 opened 6 months ago by seajane
  3

• Search for RGP membership for a list of identified proteins

  #184 opened 6 months ago by cmonat
  3

• RGP fasta

  #163 opened 6 months ago by SamVaGo
  6

• invalid type <class 'str'> for column product

  #175 opened 7 months ago by samuelmontgomery
  5

• Cannot Import GeneFinder from Pyrodigal since update

  #174 opened 7 months ago by hb660
  4

• Error since update to 2.0

  #172 opened 7 months ago by SamVaGo
  7

• ppanggolin draw --spots all don't create plots for all spots

  #129 opened 8 months ago by IsabelFE
  6

• Missing genes in the projection.tsv files

  #168 opened 8 months ago by cmonat
  2

• Projection file returns spots for genes not in RGPs

  #130 opened 8 months ago by ezherman
  3

• Comparing core genomes

  #136 opened 8 months ago by SamVaGo
  7

• Install bug

  #155 opened 8 months ago by LongXiang99
  2

• TypeError: invalid type (<class 'str'>) for column ``organism``

  #159 opened 9 months ago by raysully
  4

• Exception: The gene family has not beed associated to a partition

  #148 opened 9 months ago by JamieAlfieri
  2

• Rarefaction curves_No Heaps calculation

  #123 opened 10 months ago by jaresoles
  5

• Non-deterministic clustering (possibly due to defragmentation)

  #116 opened a year ago by apcamargo
  11

• Ignore genes during clustering

  #131 opened a year ago by Czirion
  2

• Locus tag missing from projection file

  #126 opened a year ago by ezherman
  2

• doubt about Circular contig identifiers

  #115 opened a year ago by msubirana
  4

• Attribute error drawing plots

  #121 opened a year ago by cizydorczyk
  1