fmicompbio/mutscan

Issues

• Issue using reference sequence in digestFastqs and error creating QC report

  #46 opened a year ago by shesanIsland
  7

• Only the first part of the sequence seem to be analyzed

  #42 opened 2 years ago by Ilarius
  9

• Add check that read length does not exceed the set buffer size

  #43 opened 2 years ago by csoneson
  1

• how to set par digestFastqs when my reads shorter than WT sequnce?

  #41 opened 2 years ago by mengchengyao
  4

• Replace Matrix.utils?

  #36 opened 2 years ago by csoneson
  0

• Consider breaking out the collapsing of similar sequences from `digestFastqs`

  #27 opened 3 years ago by csoneson
  1

• Rename calculatePPIScore

  #29 opened 3 years ago by csoneson
  0

• Record type of mutation?

  #28 opened 3 years ago by csoneson
  0

• Consider returning a `SummarizedExperiment` object from `digestFastqs`

  #26 opened 3 years ago by csoneson
  1

• Change default parameter values for `digestFastqs`

  #18 opened 3 years ago by csoneson
  0

• Consider exporting `.makeScatterPlot()`

  #19 opened 3 years ago by csoneson
  0

• Add number of mismatching bases/codons to SummarizedExperiment object

  #20 opened 3 years ago by csoneson
  0

• Store more annotations/properties of the variants in the SE object

  #13 opened 4 years ago by csoneson
  1

• Revisit stopping criterion/fastq output when >1 input fastq are provided

  #10 opened 4 years ago by csoneson
  2

• Add criterion to specify the length of the merged variable sequence

  #11 opened 4 years ago by csoneson
  1

• Keep only unique sequences when merging multiple experiments

  #12 opened 4 years ago by csoneson
  1

• Consider swapping atomic for reduction for incrementing counters

  #14 opened 4 years ago by csoneson
  0

• Add wrapper function for faster processing

  #2 opened 4 years ago by csoneson
  1

• Parallelize comparison to wildtype sequences

  #6 opened 4 years ago by csoneson
  1

• Export findClosestRefSeqTree

  #5 opened 4 years ago by csoneson
  0

• Add umiCollapseMinRatio parameter

  #3 opened 4 years ago by csoneson
  0