Ecosyste.ms: Issues

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GitHub / bystrogenomics/bystro issues and pull requests

#502 - WIP Random matrix theory methods

Pull Request - State: open - Opened by austinTalbot7241993 9 months ago

#501 - Sprint 12 Task List

Issue - State: open - Opened by cristinaetrv 9 months ago
Labels: .task list

#500 - update canopy to somadata

Pull Request - State: closed - Opened by akotlar 9 months ago

#498 - Add Euclidean and Riemann median calculation functions

Pull Request - State: closed - Opened by IlhaH 9 months ago

#497 - Bump setuptools from 65.5.0 to 65.5.1 in /python

Pull Request - State: open - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#496 - [infrastructure] Improve Python build process

Pull Request - State: closed - Opened by akotlar 9 months ago

#495 - Adding Documentation to deploy annotator

Pull Request - State: open - Opened by dlin30 9 months ago

#494 - fix get_user cli and api commands

Pull Request - State: closed - Opened by akotlar 9 months ago

#493 - Optimize PRS C+T preprocess for performance.

Pull Request - State: closed - Opened by cristinaetrv 9 months ago

#492 - Optimal singular value shrinkage for operator norm

Pull Request - State: closed - Opened by IlhaH 9 months ago

#491 - Add nonnegative covariance estimator and tests

Pull Request - State: closed - Opened by IlhaH 9 months ago

#490 - [annotation] Remove duplicate entries due to isCanonical

Pull Request - State: closed - Opened by akotlar 9 months ago

#489 - Add LD maps for hg38 and organize LD maps by build for PRS.

Pull Request - State: closed - Opened by cristinaetrv 9 months ago

#488 - Rare Variant Analysis Paper Compendium

Issue - State: open - Opened by akotlar 9 months ago
Labels: rare variant analysis

#487 - Add compressed versions of AD summary stats in hg19 and hg38

Pull Request - State: closed - Opened by cristinaetrv 9 months ago

#486 - [search] Improve clnsig analysis

Pull Request - State: closed - Opened by akotlar 9 months ago

#485 - Supervision Augmented PPCA

Pull Request - State: closed - Opened by austinTalbot7241993 9 months ago

#484 - Update hg19.yml database_dir to match documentation

Pull Request - State: closed - Opened by akotlar 9 months ago - 1 comment

#483 - Bump tqdm from 4.65.0 to 4.66.3 in /python

Pull Request - State: open - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#482 - [search] Add back autocomplete to CLNSIG

Pull Request - State: closed - Opened by akotlar 9 months ago - 1 comment

#481 - Add shrinkage methods

Pull Request - State: closed - Opened by IlhaH 9 months ago - 1 comment

#479 - Incorporated basic shrinkage to adversarial model

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#478 - [annotation] Add isCanonical transcript annotation

Pull Request - State: closed - Opened by akotlar 10 months ago - 1 comment

#477 - [search] Within query slice, paginate

Pull Request - State: closed - Opened by akotlar 10 months ago

#476 - Feature/no null dosage

Pull Request - State: closed - Opened by akotlar 10 months ago

#475 - Add back support for nulls in fast dosage matrix calculation

Pull Request - State: closed - Opened by akotlar 10 months ago

#474 - fix reporting of total number of filtered variants

Pull Request - State: closed - Opened by akotlar 10 months ago

#473 - Modified projection method

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago - 1 comment

#472 - Implemented commonly used losses for covariance matrix estimation

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago - 1 comment

#471 - Covariance shrinkage

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#470 - Improved initialization scheme

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#469 - Feature/ppca regularized adversarial

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#468 - Feature/domain adaptation regularized

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#467 - Soft impute CV

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago - 1 comment

#466 - #456: Add SomaScan API support

Pull Request - State: closed - Opened by akotlar 10 months ago

#465 - Covariance Module Improvements

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#464 - Bugfix marginal likelihood supervision + SVAE

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#463 - Competitor SPPCA Methods

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#462 - Fast dosage matrix filtering

Pull Request - State: closed - Opened by akotlar 10 months ago

#461 - GPU Support for PPCA

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#459 - [search] Fix save handler memory usage

Pull Request - State: closed - Opened by akotlar 10 months ago

#458 - Implementation Multitask Supervision

Pull Request - State: closed - Opened by austinTalbot7241993 10 months ago

#457 - Add hg19 version of AD GWAS summary statistics for PRS.

Pull Request - State: closed - Opened by cristinaetrv 10 months ago

#456 - Sprint 11 Task List

Issue - State: open - Opened by akotlar 10 months ago - 8 comments
Labels: .task list

#455 - remove SSR, which is not found in latest clinvar VCF

Pull Request - State: open - Opened by akotlar 10 months ago

#454 - [annotator] Improve configuration filees

Pull Request - State: closed - Opened by akotlar 11 months ago

#452 - [cli] Issue#421: API and CLI for submitting combined vcf jobs

Pull Request - State: closed - Opened by akotlar 11 months ago - 1 comment

#451 - [annotator] Issue#421 Stitch sample_list and genotype matrices

Pull Request - State: closed - Opened by akotlar 11 months ago

#450 - [search] Switch to half_float for cadd, caddIndel, and remove phyloP, phastCons

Pull Request - State: closed - Opened by akotlar 11 months ago - 1 comment

#448 - Domain Adaptation

Pull Request - State: closed - Opened by austinTalbot7241993 11 months ago

#447 - Imputation Module

Pull Request - State: closed - Opened by austinTalbot7241993 11 months ago

#446 - PyPI Bystro package

Issue - State: open - Opened by cristinaetrv 11 months ago

#445 - Bump black from 23.3.0 to 24.3.0 in /python

Pull Request - State: open - Opened by dependabot[bot] 11 months ago
Labels: dependencies, python

#444 - [annotation] Add LOFTEE and REVEL

Issue - State: open - Opened by akotlar 11 months ago
Labels: annotation

#443 - [rare variant] Add support for STAAR

Issue - State: open - Opened by akotlar 11 months ago
Labels: rare variant analysis

#441 - Issue #421: Add somascan code

Pull Request - State: closed - Opened by akotlar 11 months ago

#440 - Issue#421: Improve hg19 and hg38 opensearch index definitions

Pull Request - State: closed - Opened by akotlar 11 months ago

#439 - Issue#421: fix missing bystro-vcf fields in mapping

Pull Request - State: closed - Opened by akotlar 11 months ago

#437 - Gaussian mixture fitting of POE

Pull Request - State: closed - Opened by austinTalbot7241993 11 months ago - 1 comment

#436 - Add AD GWAS summary statistics for PRS C+T method.

Pull Request - State: closed - Opened by cristinaetrv 11 months ago - 1 comment

#435 - Feature/issue 421 remove refseq clinvar

Pull Request - State: closed - Opened by akotlar 11 months ago

#434 - Feature/streaming proteomics

Pull Request - State: closed - Opened by dlin30 11 months ago
Labels: proteomics

#433 - Issue #421: Add somascan support

Pull Request - State: closed - Opened by akotlar 11 months ago

#432 - [ancestry] Add support for choosing ancestry model with lowest missingness

Pull Request - State: closed - Opened by akotlar 11 months ago - 1 comment

#430 - [proteomics] listener

Pull Request - State: closed - Opened by dlin30 11 months ago - 1 comment

#429 - Feature/annotation interface

Pull Request - State: closed - Opened by dlin30 11 months ago - 1 comment

#428 - Issue #421: Improve OpenSearch relevance for HGVS queries

Pull Request - State: closed - Opened by akotlar 11 months ago

#426 - Rotation Domain Adaptation

Pull Request - State: closed - Opened by austinTalbot7241993 11 months ago

#425 - Add script to split vcf file by chromosome

Pull Request - State: closed - Opened by akotlar 11 months ago

#424 - [prs] Benchmark Langevin Dynamics PRS-CS against PRS-CS and SBayes-RC

Issue - State: open - Opened by akotlar 11 months ago
Labels: prs

#423 - [annotation] Stitch Together VCF Files - Second Step

Issue - State: open - Opened by akotlar 11 months ago

#422 - [ancestry] Use assembly when choosing which model to use

Issue - State: open - Opened by akotlar 11 months ago
Labels: ancestry

#421 - Sprint 9 Task List

Issue - State: open - Opened by akotlar 11 months ago - 3 comments
Labels: .task list

#419 - Send assembly version with ancestry job requests

Issue - State: open - Opened by akotlar 11 months ago
Labels: ancestry

#418 - fix perl installation documentation

Pull Request - State: closed - Opened by wingolab 11 months ago

#417 - Bugfix/ppca transform subset

Pull Request - State: closed - Opened by austinTalbot7241993 11 months ago

#416 - Bump mio from 0.8.6 to 0.8.11 in /python

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies, rust

#415 - PRS-CS with Stochastic Gradient Langevin Dynamics

Pull Request - State: closed - Opened by austinTalbot7241993 11 months ago

#414 - Add preprocess for PRS and C and T PRS calculation.

Pull Request - State: closed - Opened by cristinaetrv 11 months ago

#413 - Add initial loading and preprocess for PRS.

Pull Request - State: closed - Opened by cristinaetrv 12 months ago

#411 - [WIP] [annotation] Cleanup IO.pm

Pull Request - State: open - Opened by akotlar 12 months ago - 1 comment

#409 - WIP Feature/annotation interface

Pull Request - State: closed - Opened by dlin30 12 months ago
Labels: proteomics

#408 - Add LD maps for PRS.

Pull Request - State: closed - Opened by cristinaetrv 12 months ago - 1 comment

#407 - Add PRS to config and startup.yml

Pull Request - State: closed - Opened by cristinaetrv 12 months ago

#406 - Parent of Origin Implementation

Pull Request - State: closed - Opened by austinTalbot7241993 12 months ago

#405 - fix getChunkSize

Pull Request - State: closed - Opened by akotlar 12 months ago

#404 - Create local Ancestry cli tool

Issue - State: open - Opened by akotlar 12 months ago
Labels: ancestry

#403 - Issue #402 fast saving

Pull Request - State: closed - Opened by akotlar 12 months ago - 1 comment