BioGenies/tidysq

Issues

• I would like to add x numer of N between concatenated sequences with collapse

  #98 opened a year ago by ericgonzalezs
  2

• How do you bite rowwise?

  #97 opened 2 years ago by m3hdad
  2

• translate() uses incorrect codons for DNA to protein conversion

  #95 opened 2 years ago by poppn
  1

• Add classes to errors

  #63 opened 3 years ago by ErdaradunGaztea
  0

• Add function to apply `write_fasta` on a data frame

  #92 opened 3 years ago by danlooo
  5

• Add better check for file existence

  #91 opened 3 years ago by ErdaradunGaztea
  0

• R session crashes when searching for "^" or "$" motif

  #90 opened 3 years ago by DominikRafacz
  0

• Interpret [A, C, T, G, N] as dna_ext

  #89 opened 3 years ago by ErdaradunGaztea
  0

• CPP_sample_fasta fails when FASTA file is shorter than buffer size

  #88 opened 3 years ago by ErdaradunGaztea
  0

• add more test for options with usage of withr

  #87 opened 4 years ago by DominikRafacz
  0

• Formalize sqibble

  #83 opened 4 years ago by DominikRafacz
  2

• AMP case study

  #86 opened 4 years ago by michbur
  0

• Refactor specific types of integers (like LenSq) on C++ side

  #85 opened 4 years ago by DominikRafacz
  0

• Add more convenience parameters to `sqapply` (like `simplify`)

  #84 opened 4 years ago by DominikRafacz
  0

• Implement has_X as an analogue to remove_X

  #82 opened 4 years ago by ErdaradunGaztea
  0

• Optimize find_motifs() using some specialized string-searching algorythm

  #81 opened 4 years ago by ErdaradunGaztea
  0

• Cannot use dplyr::group_by with sq objects

  #80 opened 4 years ago by ErdaradunGaztea
  0

• Implement replace_motifs()

  #79 opened 4 years ago by ErdaradunGaztea
  0

• Include bioseq in comparisons

  #78 opened 4 years ago by ErdaradunGaztea
  0

• Calculate codon tables at compile time

  #58 opened 4 years ago by DominikRafacz
  0

• Create changelog

  #77 opened 4 years ago by ErdaradunGaztea
  0

• Add paste functionality to sq class

  #52 opened 4 years ago by ErdaradunGaztea
  2

• Add comparison and casting betwenn STD_IT and RCPP_IT objects

  #67 opened 4 years ago by DominikRafacz
  0

• Allow random_sq to use various distributions to generate lengths

  #55 opened 4 years ago by DominikRafacz
  0

• Prettify tidysq options printing

  #76 opened 4 years ago by ErdaradunGaztea
  0

• Implement exporting sq objects (or sqibbles) to LaTeX tables

  #75 opened 4 years ago by ErdaradunGaztea
  0

• Hide LetterTree, LetterNode and Motif classes from the public

  #74 opened 4 years ago by ErdaradunGaztea
  0

• Implement possibility of reading motifs for multiletter alphabets

  #61 opened 4 years ago by DominikRafacz
  0

• Cover more complicated cases of multichar alphabets packing of strings

  #70 opened 4 years ago by DominikRafacz
  1

• constructing sq with "unt" and multicharacter NA_letter fails

  #64 opened 4 years ago by ErdaradunGaztea
  3

• constructing unt sq with ignore_case = TRUE doesn't ignore case enough

  #50 opened 4 years ago by ErdaradunGaztea
  0

• export get_standard_alphabet

  #60 opened 4 years ago by DominikRafacz
  0

• Implement duplicated.sq()

  #73 opened 4 years ago by ErdaradunGaztea
  0

• Add tests for all combinations of template parameters for packing and unpacking

  #68 opened 4 years ago by DominikRafacz
  0

• Stop loading pkg::tibble upon loading tidysq

  #48 opened 4 years ago by ErdaradunGaztea
  1

• Find out if adding all possible LetterValues to value_to_letter map in alphabet results in better performance than using conditional

  #71 opened 4 years ago by DominikRafacz
  0

• Rethink the idea of unpacking NA values in string vectors

  #69 opened 4 years ago by DominikRafacz
  0

• Use template functions for packing and unpacking instead of explicitly specyfying bit shifts

  #66 opened 4 years ago by DominikRafacz
  0

• rename LVL_NONE to LVL_SILENT

  #65 opened 4 years ago by ErdaradunGaztea
  0

• Make tests for find_motifs more organized

  #54 opened 4 years ago by DominikRafacz
  0

• Handle case of codon tables with nontranslatable codons

  #62 opened 4 years ago by DominikRafacz
  0

• Rewrite format and print for sq and sq pillar shaft

  #59 opened 4 years ago by DominikRafacz
  0

• Can we call method of base class directly?

  #57 opened 4 years ago by DominikRafacz
  0

• Add safe mode for atp alphabet when constructing sq and reading_fasta

  #56 opened 4 years ago by DominikRafacz
  0

• Set LenSq as an alias for R_xlen_t

  #49 opened 4 years ago by ErdaradunGaztea
  0

• Add subclass of OperationVectorToVector that supports ResultWrapper

  #53 opened 4 years ago by DominikRafacz
  0

• Add safe_mode to import_sq()

  #44 opened 4 years ago by ErdaradunGaztea
  0

• Upgrade random to use seed and random library

  #47 opened 4 years ago by DominikRafacz
  0

• Add support for relative paths for read and write fasta

  #46 opened 4 years ago by DominikRafacz
  0

• Implement summary.sq

  #45 opened 4 years ago by ErdaradunGaztea
  0