SACGF/cdot

Issues

• API/Downloadable JSON differences?

  #87 opened 3 months ago by DGMichael
  3

• Ensembl Tark Data Provider

  #86 opened 3 months ago by davmlaw
  7

• Transcripts from NCBI/Ensembl API

  #69 opened a year ago by davmlaw
  0

• hgvs c_to_p failing with Ensembl transcript

  #82 opened 4 months ago by chubukov
  7

• Use Snakemake to build transcripts

  #70 opened a year ago by davmlaw
  7

• Ensembl files missing protein - breaking c_to_p

  #83 opened 4 months ago by davmlaw
  3

• Make a proper release

  #85 opened 4 months ago by davmlaw
  0

• FastaSeqFetcher improvements

  #84 opened 4 months ago by davmlaw
  0

• Method that returns latest data version

  #81 opened 5 months ago by davmlaw
  1

• RefSeq missing MT transcripts

  #79 opened 5 months ago by davmlaw
  6

• Ensembl 212 release

  #80 opened 5 months ago by davmlaw
  2

• JSON breaking schema changes

  #78 opened 10 months ago by davmlaw
  2

• HGNC ID still missing for some chrMT genes in ENSEMBL

  #73 opened 10 months ago by holtgrewe
  5

• CDS phase (offset for eg ribo slippage)

  #76 opened 10 months ago by holtgrewe
  5

• Document JSON.gz files, and Transcript format

  #77 opened 10 months ago by davmlaw
  0

• Clarify _<symbol> entries

  #75 opened 10 months ago by holtgrewe
  1

• Processing of mitochondrial genes RNA genes broken for ENSEMBL

  #72 opened 10 months ago by holtgrewe
  2

• Mane Plus Clinical tags missing from gff.json.gz files

  #71 opened 10 months ago by holtgrewe
  2

• Ensembl 111

  #68 opened a year ago by davmlaw
  0

• HGVS to VCF Output for HGVS nomenclature with Duplication

  #67 opened a year ago by Mchhu
  1

• Create VEP-compatible releases in CI

  #63 opened a year ago by holtgrewe
  1

• Create release vor VEP110

  #58 opened a year ago by holtgrewe
  1

• Split code and data releases?

  #64 opened a year ago by holtgrewe
  5

• Retrieving duplicate exons from UTA for some transcripts

  #56 opened a year ago by davmlaw
  2

• Properly tag selenoproteins

  #66 opened a year ago by holtgrewe
  2

• Note: PRSS2 / HGNC:9483 missing from cdot v0.2.21 GRCh37/RefSeq

  #59 opened a year ago by holtgrewe
  3

• cdot 0.2.21 NM_007294.4 is missing protein ID NP_009225.1 on GRCh38

  #60 opened a year ago by holtgrewe
  0

• Add tests to CI

  #62 opened a year ago by holtgrewe
  0

• "NM_138693.4" json generation error

  #57 opened a year ago by ltnetcase
  4

• FastaSeqFetcher - investigate differences between refseq and fasta exon generated transcript

  #55 opened a year ago by davmlaw
  1

• Historical GRCh38 refseq

  #51 opened a year ago by davmlaw
  3

• UTA to cdot transcript start/end conversion issue

  #53 opened a year ago by davmlaw
  1

• FastaSeqFetcher - handle deletions

  #45 opened 2 years ago by davmlaw
  2

• Diff coding coordinates from latest

  #54 opened a year ago by davmlaw
  0

• Ensembl 110

  #52 opened a year ago by davmlaw
  1

• Biotype - missing in Ensembl transcripts

  #50 opened a year ago by davmlaw
  1

• MT not converted to contigs correctly (GRCh37/Ensembl only)

  #49 opened 2 years ago by davmlaw
  0

• get_tx_exons - return extra fields if possible

  #48 opened 2 years ago by davmlaw
  1

• get_tx_info should properly handle alt_ac and alt_aln_method

  #46 opened 2 years ago by davmlaw
  1

• Implement get_alignments_for_region

  #47 opened 2 years ago by davmlaw
  2

• Support for non-human species

  #44 opened 2 years ago by davmlaw
  0

• Ensembl T2T - CHM13v2 GTF

  #42 opened 2 years ago by davmlaw
  0

• Contigs not converted to accession numbers properly

  #43 opened 2 years ago by davmlaw
  0

• Support T2T

  #41 opened 2 years ago by davmlaw
  1

• Explain file downloads

  #40 opened 2 years ago by holtgrewe
  4

• Fasta file SeqFetcher implementation

  #39 opened 2 years ago by davmlaw
  2

• Provide python-attrs classes?

  #37 opened 2 years ago by holtgrewe
  1

• Differing implementation of get_tx_for_region to hgvs one

  #38 opened 2 years ago by holtgrewe
  3

• Transcript aliases - HGVS using gene names (canonical transcripts) or LRG

  #36 opened 2 years ago by davmlaw
  2

• Tags (ie MANE Select / RefSeq select etc) should be genome build specific

  #35 opened 2 years ago by davmlaw
  0