rockt/SETH

Issues

• Convert dbSNP into TSV-files: ParseJSONToFile.java misses HGVS names

  #45 opened 2 years ago by sg-wbi
  3

• Unable to run NEN example

  #39 opened 3 years ago by yuanhao96
  2

• Error: cannot find or fail to load the main class de.hu.berlin.wbi.stuff.dbSNPParser.xml.ParseXMLToFile when Parse dbSNP-XML dump

  #36 opened 3 years ago by QQ-Peng
  4

• Add flag to identify synonymous variations

  #35 opened 3 years ago by Erechtheus
  0

• Detect ss-sequences

  #34 opened 3 years ago by Erechtheus
  0

• Use Mutalyzer or hgvs for variant normalization

  #32 opened 3 years ago by Erechtheus
  0

• Parse dbSNP from JSON and no longer from XML

  #31 opened 4 years ago by Erechtheus
  1

• How to run faster ？

  #29 opened 4 years ago by YaoXinZhi
  8

• Database '/path/to/derby/database/dbSNP137' not found.

  #28 opened 4 years ago by YaoXinZhi
  2

• Bug Report, wrong offset.

  #30 opened 4 years ago by YaoXinZhi
  2

• Additional evaluation corpus (Amia18)

  #23 opened 6 years ago by Erechtheus
  0

• Improve named entity normalization using patterns

  #21 opened 7 years ago by Erechtheus
  1

• Improve entity normalization using more HGVS mentions

  #22 opened 7 years ago by Erechtheus
  0

• Additional evaluation corpus (TMVar 2.0)

  #20 opened 7 years ago by Erechtheus
  0

• Write BRAT compatible annotations

  #19 opened 7 years ago by Erechtheus
  0

• Linguistic mapping of mutations to genes

  #14 opened 8 years ago by jhkbg
  0

• Additional evaluation corpora (Nala)

  #18 opened 7 years ago by Erechtheus
  0

• Logging

  #16 opened 8 years ago by Erechtheus
  0

• BioC integration

  #8 opened 8 years ago by Erechtheus
  1

• Incorrect rsIds and no extracted rsIds

  #17 opened 8 years ago by spenagon
  1

• MutationMention.toHGVS() returns '??' for entities already following the HGVS c. and m. notation

  #13 opened 8 years ago by jhkbg
  1

• Map variants down to chromosomal location + allele

  #15 opened 8 years ago by jhkbg
  0

• Incorrectly extracted mutations

  #10 opened 8 years ago by jhkbg
  2

• HGVS c/p copied to invalid transcripts for overlapping genes

  #12 opened 8 years ago by jhkbg
  3

• Insdels are classified as type "null"

  #7 opened 8 years ago by Erechtheus
  0

• Wrong mutation type recognized

  #6 opened 8 years ago by Erechtheus
  0

• Additional evaluation corpora (Bronco)

  #9 opened 9 years ago by Erechtheus
  0

• SNP-Gene association

  #1 opened 10 years ago by Erechtheus
  0

• Extract underspecified mutations

  #2 opened 11 years ago by rockt
  1

• Increase SETH's coverage of mutations contained HGVS

  #4 opened 11 years ago by rockt
  1

• Insdels can also be written using >

  #3 opened 11 years ago by rockt
  0