r2dt-bio/R2DT

Issues

• Add domain labels to templates

  #160 opened a month ago by AntonPetrov
  4

• Some large single stranded regions incorrectly removed as insertions

  #162 opened a month ago by nawrockie
  1

• Input sequence names identical to sequence name in Rfam alignment will cause R2DT to fail

  #161 opened a month ago by nawrockie
  0

• Refactor the core visualise function

  #159 opened a month ago by AntonPetrov
  0

• Improve visibility of numbering labels and numbering lines

  #158 opened 2 months ago by AntonPetrov
  0

• Feature request: Download RNA2D schema from R2DT widget

  #101 opened 2 months ago by Psirving
  6

• Do not require users to install precomputed library

  #151 opened 3 months ago by AntonPetrov
  0

• Improve installation process

  #147 opened 4 months ago by AntonPetrov
  0

• Make sure editors support pseudoknots

  #154 opened 3 months ago by AntonPetrov
  0

• Add a wrapper command for enrich_json and json2svg

  #153 opened 3 months ago by AntonPetrov
  0

• Prevent tRNAs from matching non-tRNA Rfam models

  #152 opened 3 months ago by AntonPetrov
  0

• View structures with pseudoknots

  #91 opened 3 months ago by VonBoss
  6

• Checklist for release 2.1

  #150 opened 3 months ago by AntonPetrov
  0

• Checklist for release 2.0

  #145 opened 3 months ago by AntonPetrov
  0

• Bundle Rfam seeds into cms tarball?

  #124 opened 3 months ago by afg1
  2

• Speed up template selection using Ribovore + Blast

  #115 opened 3 months ago by AntonPetrov
  0

• Possible R2DT bug

  #149 opened 3 months ago by ValWood
  3

• Possible off-by-one error?

  #121 opened 3 months ago by pzhaojohnson
  1

• Create animated 2Ds showing transition between 2D structures from PDB files

  #146 opened 4 months ago by AntonPetrov
  0

• Checklist for release 1.4

  #86 opened 4 months ago by AntonPetrov
  0

• Temp file collision causing cluster jobs to hang

  #96 opened 4 months ago by afg1
  3

• Use RiboCentre diagrams as templates

  #143 opened 4 months ago by AntonPetrov
  0

• outdated link to CRW2: Comparative RNA Web-2

  #138 opened 6 months ago by ValWood
  0

• Considerations for external implementations of R2DT widget

  #137 opened 6 months ago by ValWood
  6

• Switch to relative coordinates

  #131 opened a year ago by AntonPetrov
  6

• Use Typer and Rich

  #133 opened a year ago by AntonPetrov
  0

• Improve thumbnail images

  #130 opened a year ago by AntonPetrov
  0

• Add --verbose option to control reporting

  #114 opened a year ago by AntonPetrov
  0

• Update Traveler to latest version

  #128 opened a year ago by AntonPetrov
  0

• Improve handling of sequences with MultipleHits warnings

  #125 opened a year ago by AntonPetrov
  0

• Use --detail option with tRNAscan-SE

  #97 opened 2 years ago by patriciaplchan
  0

• Switch to Python API where possible

  #113 opened a year ago by AntonPetrov
  0

• Update tRNA models

  #83 opened a year ago by AntonPetrov
  0

• Update Type T RNase P RNA templates

  #84 opened a year ago by AntonPetrov
  1

• Integrate with RNAFramework

  #108 opened a year ago by AntonPetrov
  0

• Use JSON Schema for creating new templates

  #77 opened a year ago by AntonPetrov
  1

• Secondary feature annotations (helix, ES, etc)

  #107 opened a year ago by joegeorgeson
  2

• Host docs on RTD

  #88 opened a year ago by AntonPetrov
  1

• Include name in json schema output

  #100 opened 2 years ago by AntonPetrov
  0

• Models missing in R2DT v1.3 cms

  #99 opened 2 years ago by afg1
  1

• Use alignments from tRNAscan-SE without re-creating them in R2DT

  #98 opened 2 years ago by patriciaplchan
  0

• Infernal mapping not working for "depaired" and "constrained" structures

  #93 opened 2 years ago by AntonPetrov
  0

• Use more precise SO terms for mt rRNAs

  #87 opened 2 years ago by blakesweeney
  0

• Checklist for release 1.3

  #82 opened 2 years ago by AntonPetrov
  0

• Add a flag to override ribovore filters

  #75 opened 2 years ago by AntonPetrov
  0

• r2dt/traveller segfault for some sequences/models

  #81 opened 2 years ago by afg1
  3

• R2DT does not generate a 2D for URS000026BDF0_9606

  #79 opened 2 years ago by blakesweeney
  2

• Store constrained folding and fold type info in tsv

  #80 opened 2 years ago by carlosribas
  0

• Create an option to display full sequence in Traveler's layout

  #78 opened 3 years ago by aspetr01
  0

• Label each nucleotide in SVG with the index of input sequence

  #76 opened 3 years ago by blakesweeney
  3