kfuku52/amalgkit

Issues

• Adding delta PCC to AMALGKIT output

  #152 opened 6 months ago by Hego-CCTB
  4

• Code for rRNA rate

  #145 opened 6 months ago by kfuku52
  2

• curate_group -> sample_group

  #151 opened a year ago by kfuku52
  3

• Output uncorrected tables without going through all of curate

  #147 opened a year ago by Hego-CCTB
  3

• Duplication rate and insert size peak from the fastp json report

  #150 opened a year ago by kfuku52
  0

• merge plot

  #136 opened a year ago by kfuku52
  1

• Effect of negative value clipping in log(x+1) values

  #139 opened a year ago by kfuku52
  1

• use seqkit instead of pigz to compress fastq

  #138 opened a year ago by kfuku52
  0

• Metadata example command

  #149 opened a year ago by docxology
  3

• cstmm - curate incompatibility

  #148 opened a year ago by kfuku52
  4

• Error in if (child1_color == child2_color) { :

  #146 opened 2 years ago by kfuku52
  0

• Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

  #144 opened 2 years ago by kfuku52
  0

• Obsoleting search_term_*.config

  #143 opened 2 years ago by kfuku52
  3

• amalgkit curate --h

  #142 opened 2 years ago by docxology
  1

• ValueError: No objects to concatenate

  #141 opened 2 years ago by kfuku52
  0

• amalgkit getfastq on folder with already-processed samples is re-running

  #135 opened 2 years ago by docxology
  13

• FutureWarning: The argument 'infer_datetime_format' is deprecated and will be removed in a future version.

  #140 opened 2 years ago by kfuku52
  1

• mapping rate and cstmm factor in the curate SV predictive power plot

  #137 opened 2 years ago by kfuku52
  1

• getfastq OSError: [Errno 5] Input/output error:

  #134 opened 2 years ago by docxology
  1

• broken csca

  #130 opened 2 years ago by kfuku52
  1

• PCA with missing data

  #125 opened 2 years ago by kfuku52
  1

• print('layout = {}; Deleting unpaired file: {}'.format(sra_stat['layout'], unpaired_file)) NameError: name 'unpaired_file' is not defined

  #133 opened 2 years ago by docxology
  3

• is_unpaird_file --> is_unpaired_file?

  #132 opened 2 years ago by docxology
  1

• fastq-dump.2.8.0 err: column not found while opening table within short read archive module

  #131 opened 2 years ago by docxology
  3

• species-wise curate subdirectories

  #124 opened 2 years ago by kfuku52
  0

• Error in data.frame(curate_group = curate_group_u, curate_group_color = curate_group_color[1:length(curate_group_u)],

  #129 opened 2 years ago by kfuku52
  6

• NameError: name 'work_dir' is not defined

  #128 opened 2 years ago by kfuku52
  3

• FileNotFoundError

  #127 opened 2 years ago by kfuku52
  6

• restructure and simplify `metadata`

  #126 opened 2 years ago by kfuku52
  2

• removing unnecessary dependencies

  #120 opened 2 years ago by kfuku52
  3

• clean up csca.R

  #119 opened 2 years ago by kfuku52
  4

• BUSCO-based csca

  #123 opened 2 years ago by kfuku52
  1

• sanity --updated_metadata_dir

  #121 opened 2 years ago by kfuku52
  2

• cstmm: directly specifying --orthogroup_table instead of OrthoFinder directory with --ortho

  #122 opened 2 years ago by kfuku52
  1

• Obsoleting short options

  #117 opened 2 years ago by kfuku52
  1

• Semantic versioning

  #118 opened 2 years ago by kfuku52
  1

• amalgkit config writing files out of place

  #116 opened 2 years ago by kfuku52
  5

• pandas.errors.IntCastingNaNError: Cannot convert non-finite values (NA or inf) to integer

  #115 opened 2 years ago by kfuku52
  19

• --config_dir

  #109 opened 2 years ago by kfuku52
  1

• Obsoleting updated_metadata

  #103 opened 2 years ago by kfuku52
  14

• Error when a config file is missing

  #108 opened 2 years ago by kfuku52
  5

• getfastq download options

  #111 opened 2 years ago by kfuku52
  2

• quant --id

  #112 opened 2 years ago by kfuku52
  2

• amalgkit integrate assigns wrong file paths

  #114 opened 2 years ago by kfuku52
  1

• sys.stderr.write('ERROR: could not find fastq file(s) in:', output_dir_getfastq)

  #113 opened 2 years ago by kfuku52
  1

• pandas.errors.IntCastingNaNError: Cannot convert non-finite values (NA or inf) to integer

  #110 opened 2 years ago by kfuku52
  1

• amalgkit config

  #104 opened 2 years ago by kfuku52
  10

• pandas 1.5

  #106 opened 2 years ago by kfuku52
  14

• No expression data found. Please make sure `amalgkit merge` or `amalgkit cstmm` ran correctly and you provided the correct directory path

  #107 opened 2 years ago by kfuku52
  0

• pandas.errors.EmptyDataError: No columns to parse from file

  #105 opened 2 years ago by kfuku52
  0