RasmussenLab/phamb

Issues

• category of viruses identified by PHAMB ?

  #61 opened 5 months ago
  0

• Can PHAMB be used directly for Virome analysis (enrichment of viral particles followed by sequencing)

  #60 opened 6 months ago
  2

• interpret the results of RF model

  #59 opened 6 months ago
  0

• How to Run - not in parallel - quick and dirty

  #58 opened 6 months ago
  1

• VAE or AAE?

  #57 opened 7 months ago
  1

• how to get the file 'clusters.tsv' ?

  #56 opened 9 months ago
  0

• 'run_RF.py' operation problem

  #55 opened 9 months ago
  1

• Binning question, how to use vamb?

  #54 opened 9 months ago
  7

• The predicted 'viral' number in 'vambbins_RF_predictions.txt' is inconsistent with the actual number in 'vamb_bins.1.fna'?

  #53 opened 9 months ago
  1

• What are the criteria of RF model

  #52 opened 9 months ago
  2

• how to evaluate the bin-annotations?

  #51 opened 9 months ago
  1

• split_contigs.py produces empty files

  #50 opened 9 months ago
  2

• Can PHAMB output comparable performance on environmental metagenome compared to gut metagenome

  #49 opened 9 months ago
  1

• split_contigs.py produces empty files

  #48 opened 6 months ago
  1

• High number of bacterial genes in phamb assembled bins

  #47 opened 9 months ago
  3

• Update shebang lines in phamb python scripts

  #46 opened 2 years ago
  2

• contig length

  #45 opened 2 years ago
  1

• Parsing deepvirfinder line 512, in _parse_dvf_row contig_name, length, score, pvalue = line[:-1].split()

  #43 opened 2 years ago
  2

• Versioned release package for Phamb

  #42 opened 2 years ago
  16

• modified header names in PHAMB

  #41 opened 2 years ago
  4

• Question about the workflow

  #40 opened 2 years ago
  0

• Including micomplete Arch131 and/or VIBRANT annotations?

  #39 opened 2 years ago
  1

• Empty or outcommented file

  #37 opened 2 years ago
  1

• Running Phamb without reads

  #36 opened 2 years ago
  1

• Vcheck on predicted viral bins

  #35 opened 2 years ago
  4

• Suggestion : add checkv step beforehand to remove complete genomes

  #34 opened 2 years ago
  2

• Random Forest Feature Names

  #33 opened 2 years ago
  1

• Running vamb/phamb using only Vibrant contigs

  #32 opened 2 years ago
  3

• How can I control the total number of threads used by phamb?

  #31 opened 2 years ago
  1

• Result assessment!

  #30 opened 2 years ago
  9

• Running Phamb on long reads polished with short reads

  #29 opened 2 years ago
  1

• Adapt for more recent Python versions.

  #28 opened 2 years ago
  0

• Issues about the installation of dependence

  #27 opened 2 years ago
  5

• Error while running RF model

  #26 opened 2 years ago
  5

• Suggesting changes to dvf.yaml

  #22 opened 3 years ago
  0

• MAGs?

  #21 opened 2 years ago
  1

• pbs vs sh

  #1 opened 4 years ago
  0