bystrogenomics/bystro

Issues

• PRS Task List

  #313 opened 7 months ago
  3

• [perl] Evaluate reading file headers to deduce compression types

  #312 opened a year ago
  0

• Poll for index availability post search indexing

  #307 opened a year ago
  1

• Annotation Sprint 3 Task List

  #302 opened a year ago
  1

• Consider renaming master branch to main

  #297 opened a year ago
  2

• Update bystro docker server

  #296 opened a year ago
  0

• Update installation documentation

  #295 opened a year ago
  0

• Clean project branches

  #294 opened a year ago
  1

• When no annotation files present, bin/bystro-build.pl will not error

  #285 opened a year ago
  0

• Send Carsten API docs

  #284 opened a year ago
  1

• Make tar OS-agnostic in perl code

  #282 opened a year ago
  0

• Stand up worker for PRS model

  #280 opened 2 months ago
  0

• Ingest association scores file for PRS

  #279 opened 2 months ago
  0

• linux and macosx use two incompatible tar implementations, leading to bugs on macosx

  #277 opened a year ago
  0

• Annotation Sprint 2 Task List

  #273 opened a year ago
  3

• Backend: Ensure that overlap delimiter is properly replaced with another character during database build. Write unit test to prove correctness if one doesn't exist

  #263 opened a year ago
  2

• Review unit tests, add unit tests where appropriate / time permitting (best effort)

  #262 opened a year ago
  0

• Documentation: Get consensus on how to handle the overlap delimiter. Control character seems problematic

  #261 opened a year ago
  1

• DB Build: Update hg19 database with other missing b10 database tracks/features (CADD already in)

  #260 opened a year ago
  2

• DB Build: Update hg38 database with CADD & other missing b10 database tracks / features

  #259 opened a year ago
  4

• Documentation: CLI bystro users can already select subsets of annotation, by editing the YAML config file for the assembly in use. Document how to do this.

  #258 opened a year ago
  2

• Webapp: Allow user to select subset of annotations, with a "Minimal" set that can be selected in the frontend

  #257 opened a year ago
  0

• Documentation: Gather feedback on annotations to add for V1.0.0 release (do we add all gnomad annotations, etc)

  #256 opened a year ago
  2

• Share results with Dave & ask him about Austin's N condition simulator proposal

  #254 opened a year ago
  1

• PR Adversarial model: maximizes explained, minimizes predictive ability on confounding variables.

  #253 opened 8 months ago
  0

• Test the same models on our N>3 condition simulation and write down results

  #252 opened 8 months ago
  0

• Test the existing models (Reduced Rank Regression, EM ZIP TADA, ML TADA, Dirichlet Process TADA) on Dave's simulations, record performance

  #251 opened a year ago
  1

• Generate realistic simulations on Dave's 2 condition simulation

  #250 opened a year ago
  1

• Get underlying statistical model for Dave's simulation written out

  #249 opened 10 months ago
  2

• GWAS - Stand up worker for GWAS model

  #248 opened a year ago
  0

• Ingest covariate and phenotype files for GWAS

  #247 opened a year ago
  0

• Documentation: Find/select 1 PRS module to implement/port

  #246 opened 9 months ago
  1

• Documentation: Find/select 1 GWAS module to implement / port to Bystro

  #245 opened a year ago
  0

• Ancestry - Deployment tests for ancestry model

  #244 opened 9 months ago
  0

• GWAS Task List

  #243 opened a year ago
  0

• Annotation Sprint 1 Task List

  #241 opened a year ago
  1

• Ingest combined protein abundance file

  #238 opened a year ago
  0

• Query annotation index by regions extracted from RefSeq Index

  #234 opened a year ago
  0

• Query RefSeq Index By Gene Extracted From TMT Protein Abundance File

  #233 opened a year ago
  0

• Query refSeq / region track by gene label from combined protein abundance file

  #232 opened 8 months ago
  1

• Ingest refSeq / region track of choice defined in hg19.yml / hg38.yml into opensearch

  #231 opened a year ago
  0

• Query by padded refSeq region instead of directly on annotation

  #230 opened a year ago
  0

• Filter protein abundance data on queried annotation output

  #229 opened 9 months ago
  0

• Query annotation by gene labels (using slice query)

  #228 opened a year ago
  1

• [task list][ml] Rare Variant Analysis Task List

  #227 opened 8 months ago
  1

• Create protein abundance filtering batch submission python API beanstalkd listener/handler

  #226 opened a year ago
  1

• Pull out gene labels from protein abundance data

  #225 opened a year ago
  0

• Adversarial TADA model

  #224 opened a year ago
  0

• [task list][proteomics] Protein Abundance Task List

  #223 opened a year ago
  1

• Can't respond for some reason. It doesn't need a path, these are being saved as model attributes like in sklearn

  #222 opened a year ago
  0