labgem/PPanGGOLiN

Issues

• PPanGGOLiN hangs when partitioning does not work

  #114 opened a year ago
  11

• Spot Plot Error

  #109 opened a year ago
  2

• Identity/coverage threshold for species/genus?

  #108 opened a year ago
  1

• Deprecated NumPy

  #107 opened 2 years ago
  7

• Attribute error when draw spots

  #106 opened 2 years ago
  2

• Only extract gene families within RGPs

  #104 opened 10 months ago
  5

• Extract gene IDs located within RGPs

  #103 opened a year ago
  6

• Error when re-partitionning a .h5 file obtained from the panmodule subcommand

  #102 opened 2 years ago
  1

• PPanGGOLiN taking too much time to run on large collection of genomes

  #101 opened 2 years ago
  6

• less genes clustered than genes in the pangenome

  #100 opened 2 years ago
  7

• How to extract the genome location of the spots

  #99 opened 2 years ago
  2

• Plastic regions

  #98 opened 2 years ago
  1

• drawing some spot is not working ValueError

  #97 opened 2 years ago
  9

• Searching for spots using the gene as a query

  #96 opened 2 years ago
  8

• Error in WriteBinaries.py

  #95 opened a year ago
  19

• Spots - way to get the flanking genes?

  #94 opened 2 years ago
  3

• Position column in pangenomeGraph.json file

  #93 opened 2 years ago
  4

• Regions of Genome Plasticity

  #92 opened 2 years ago
  2

• What does this column mean?

  #91 opened 2 years ago
  1

• Shell partitions

  #90 opened 2 years ago
  16

• Running PPanGGOLiN on larger data

  #89 opened 2 years ago
  8

• Not sure how to use genomic context option

  #88 opened 2 years ago
  8

• huge difference in results with --fasta and --anno, question

  #87 opened 2 years ago
  3

• issue with ppanggolin cluster

  #86 opened a year ago
  19

• Only extract unique RGPs

  #84 opened 2 years ago
  2

• plasmid/phage genomes

  #82 opened 2 years ago
  10

• Hierarchical Clustering

  #81 opened 2 months ago
  6

• Partitioning

  #80 opened 3 years ago
  9

• Phylogeny Question

  #79 opened 2 years ago
  1

• User-Defined Filtering and Annotation

  #78 opened 2 years ago
  3

• Suggestion : Add length gene on Bokeh Spot frame

  #77 opened 2 years ago
  2

• Data of gexf/light_gexf I can get

  #76 opened 2 years ago
  3

• Install without Conda

  #74 opened 2 years ago
  4

• compatibility with newest compiler

  #69 opened 3 years ago
  1

• Merge pangenome graphs

  #68 opened 3 years ago
  5

• Any Tips on Making a Pangenome on Genetically Disparate Species?

  #67 opened 3 years ago
  1

• Problem of file format with Bakta

  #66 opened 3 years ago
  1

• Persistent gene families query

  #62 opened 3 years ago
  6

• Unable to Render graph using RAST Annotations #44--FOLLOW UP

  #61 opened 3 years ago
  11

• Ppackage ppanggolin-v0.3.88-py37h01d97ff_0 requires pytables 3.5.*, but none of the providers can be installed

  #60 opened 3 years ago
  5

• conda/mamba pyhton_abi problems

  #59 opened 4 years ago
  9

• add the possibility to use 'align' even when the clustering is not performed through PPanGGOLiN

  #58 opened 2 months ago
  2

• Enhance drawing spot in plot

  #57 opened 3 years ago
  3

• Importing Anvio Pangenomic gene clusters into PPAnGGOLiN

  #56 opened 3 years ago
  38

• Format for MY_CLUSTERS_FILE

  #55 opened 4 years ago
  3

• Gff3 and gbk files will not work but fasta does

  #54 opened 4 years ago
  5

• Locus Tags vs Gene_ids

  #53 opened 4 years ago
  6

• nucleotide or protein clustering?

  #52 opened 3 years ago
  2

• gbk file is not work!

  #51 opened 4 years ago
  4

• Minimum and maximum number of organism for rarefaction curve

  #50 opened 4 years ago
  2