ELELAB/cancermuts

Issues

• Assertion in genomic coordinate conversion makes cancermuts crash

  #201 opened 2 months ago by mtiberti
  1

• crash when trying to plot metatable with specific ELMs

  #199 opened 2 months ago by mtiberti
  0

• add support for `gget.elm` to supply ELM predictions

  #197 opened 7 months ago by mtiberti
  0

• Change Biopython three_to_one to three_to_index

  #194 opened 7 months ago by katmeld
  0

• The README file doesn't list all the supported annotations/databases

  #177 opened 7 months ago by mtiberti
  0

• Add genomic coordinates to sequence

  #193 opened 8 months ago by katmeld
  0

• Add link to cancermuts online database to README

  #191 opened 9 months ago by mtiberti
  0

• Files downloaded from web server don't have the right content

  #190 opened a year ago by mtiberti
  1

• Turns cancermuts webpage into cancermuts website

  #188 opened a year ago by mtiberti
  0

• Add preliminary version of web app for Cancermuts

  #182 opened a year ago by mtiberti
  0

• `cancermuts.Table.plot_metatable` should support partial tables

  #186 opened a year ago by mtiberti
  0

• make website and database compliant with licenses of our data sources

  #184 opened a year ago by mtiberti
  0

• Keep track and store relevant IDs as metadata when downloading mutations

  #185 opened a year ago by mtiberti
  0

• Sequence download should prioritise Uniprot AC vs Uniprot ID

  #180 opened a year ago by mtiberti
  0

• gnomAD fails when calculating `popmax` and all populations are `NaN`

  #178 opened a year ago by mtiberti
  1

• REVEL retrieval crashes in some instances

  #175 opened a year ago by mtiberti
  1

• REVEL retrieval crashes when multiple REVEL scores for a genomic mutations are present

  #173 opened a year ago by mtiberti
  0

• COSMIC() crashes when no file is specified

  #169 opened 2 years ago by katmeld
  1

• Crash when doing ELM predictions

  #167 opened 2 years ago by katmeld
  2

• Issues with MobiDB and API switch

  #158 opened 2 years ago by mtiberti
  0

• We should add popmax annotation to gnomAD

  #146 opened 2 years ago by mtiberti
  0

• Crash when trying to add genomic mutations for VHL

  #163 opened 2 years ago by mtiberti
  1

• Crash when plotting metatable

  #165 opened 2 years ago by mtiberti
  1

• ELM accession numbers to add to metatable

  #147 opened 2 years ago by elenapapaleo
  2

• failure to retrieve UniProt sequence is not handled gracefully

  #160 opened 2 years ago by mtiberti
  0

• gNOMAD annotation crashes if no gNOMAD variants are available

  #156 opened 2 years ago by mtiberti
  0

• error with cancermuts (pancancer+clinvar) on ATG4A

  #151 opened 2 years ago by mattu90
  1

• `numpy` type aliases have been removed from recent numpy

  #153 opened 2 years ago by mtiberti
  1

• problems with genes with '-' in the name

  #150 opened 2 years ago by elenapapaleo
  3

• change the way we label the manual annotation

  #148 opened 2 years ago by elenapapaleo
  1

• "The server didn't come up." error message when try to run pancancer.py for the TXN gene

  #152 opened 2 years ago by marnaudi
  1

• Annotations of N-linked glycosylations

  #149 opened 2 years ago by MatteoLambrughi
  0

• change order of columns in metatable

  #136 opened 2 years ago by elenapapaleo
  0

• column titles aren't very computer-friendly

  #143 opened 2 years ago by mtiberti
  0

• Sometimes cBioPortal doesn't return an answer to our queries

  #135 opened 2 years ago by mtiberti
  0

• Not being able to retrieve a MobiDB prediction can result in an unhandled exception

  #140 opened 2 years ago by mtiberti
  0

• cBioPortal can't initialize Swagger client

  #137 opened 2 years ago by mtiberti
  0

• Plotting fails when multiple REVEL scores are found in the table

  #133 opened 2 years ago by mtiberti
  0

• ELM interrogation should wait for three minutes before running

  #131 opened 2 years ago by mtiberti
  1

• missing data ambra1

  #127 opened 2 years ago by elenapapaleo
  1

• Changes in UniProt API makes it impossible to retrieve Sequence data

  #129 opened 2 years ago by mtiberti
  0

• Figure generation fails when REVEL column is dtype object

  #124 opened 2 years ago by mtiberti
  0

• Cancermuts lack a way to plot structured regions from MobiDB

  #121 opened 2 years ago by mtiberti
  0

• Phosphosite fails to locate default database files

  #118 opened 2 years ago by mtiberti
  0

• gnomAD annotates `None` allele frequency instead of not annotating

  #116 opened 2 years ago by mtiberti
  1

• default separator in CSV for ManualAnnotation should be `;`

  #114 opened 2 years ago by mtiberti
  1

• MobiDB should have better default alias for sequences

  #112 opened 2 years ago by mtiberti
  1

• gnomAD sometimes displays `nan`allele frequencies

  #110 opened 2 years ago by mtiberti
  0

• ELM should have a default alias specified

  #108 opened 2 years ago by mtiberti
  0

• PhsopshoSite should allow costum file names for database

  #106 opened 2 years ago by mtiberti
  1