Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / aehrc/VariantSpark issues and pull requests

#241 - Issue/237

Pull Request - State: open - Opened by NickEdwards7502 4 months ago
Labels: enhancement, dependencies, java, python

#240 - hail dependency issue

Pull Request - State: closed - Opened by ChristinaXu2017 5 months ago - 1 comment

#239 - au.csiro.aehrc.third.hail-is issue

Issue - State: closed - Opened by ChristinaXu2017 5 months ago - 1 comment

#238 - Load vcf bgz

Pull Request - State: closed - Opened by ChristinaXu2017 10 months ago

#237 - Make VS hail independent for the python API

Issue - State: open - Opened by rocreguant 12 months ago

#236 - Fix the readme links and video

Issue - State: closed - Opened by rocreguant 12 months ago - 1 comment

#235 - Bump org.apache.spark:spark-core_2.12 from 3.1.2 to 3.3.2.3.3.7180.12-5

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, java

#234 - Bump scipy from 1.6.3 to 1.10.0 in /python

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#233 - Bump scipy from 1.6.3 to 1.10.0 in /dev

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#232 - Install on any machine throws ``` java.lang.IncompatibleClassChangeError```

Issue - State: closed - Opened by surak over 1 year ago - 1 comment

#230 - Reporting a vulnerability

Issue - State: closed - Opened by igibek almost 2 years ago

#229 - fit_trees() unable to run due to IncompatibleClassChangeError

Issue - State: closed - Opened by chrysania almost 2 years ago - 2 comments

#228 - Can we remove the Hail monkey patches after this Hail PR?

Issue - State: closed - Opened by danking almost 2 years ago - 1 comment

#227 - Bump htsjdk from 2.21.0 to 3.0.1

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, java

#226 - Bump pyspark from 3.1.3 to 3.2.2 in /python

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, python

#225 - Bump pyspark from 3.1.3 to 3.2.2 in /dev

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, python

#224 - run on single chromosomes?

Issue - State: closed - Opened by sshanshans about 2 years ago - 1 comment

#223 - organizing the notebooks, and adding the new azure ones

Pull Request - State: closed - Opened by rocreguant over 2 years ago

#222 - removing unnecessary cells

Pull Request - State: closed - Opened by rocreguant over 2 years ago

#221 - adding automatic splitCount threshold selection function

Pull Request - State: closed - Opened by rocreguant over 2 years ago

#220 - update hail init with spark context

Pull Request - State: closed - Opened by rocreguant over 2 years ago

#219 - Bump numpy from 1.21.2 to 1.23.0 in /python

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, python

#218 - Bump numpy from 1.21.2 to 1.23.0 in /dev

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, python

#217 - HADOOP ERROR SERVICE AWS....

Issue - State: closed - Opened by cmorris2945 over 2 years ago - 9 comments

#216 - How to use vcf file?

Issue - State: closed - Opened by cmorris2945 over 2 years ago - 4 comments

#215 - Simplifying the maven relase and related github actions.

Pull Request - State: closed - Opened by piotrszul over 2 years ago

#213 - updated POM

Pull Request - State: closed - Opened by rocreguant over 2 years ago - 1 comment

#212 - Bump numpy from 1.21.2 to 1.22.0 in /python

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies, python

#211 - Bump numpy from 1.21.2 to 1.22.0 in /dev

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies, python

#210 - Bump pyspark from 3.1.2 to 3.1.3 in /python

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, python

#209 - Covariates implementation and interface

Pull Request - State: closed - Opened by rocreguant almost 3 years ago

#208 - Implements p-value calculation from python

Pull Request - State: closed - Opened by rocreguant almost 3 years ago

#207 - [#201] Implements p-value (test)

Pull Request - State: closed - Opened by piotrszul almost 3 years ago - 1 comment

#206 - Add split variable count to hail output.

Pull Request - State: closed - Opened by piotrszul over 3 years ago

#205 - Add split variable count to hail output

Issue - State: closed - Opened by piotrszul over 3 years ago

#204 - optimise VariantSpark for large sample size (n>50K)

Issue - State: open - Opened by natwine over 3 years ago - 1 comment

#203 - Update to Spark 3.1 and Hail 0.2.74

Pull Request - State: closed - Opened by piotrszul over 3 years ago

#202 - python script to extract split variable counts from rf json model

Pull Request - State: closed - Opened by piotrszul over 3 years ago

#201 - automate pvalue calculation in VariantSpark pipeline

Issue - State: closed - Opened by natwine over 3 years ago

#200 - Migrate to Spark 3.1

Issue - State: closed - Opened by piotrszul over 3 years ago - 1 comment

#199 - Add variable count extraction from json model

Issue - State: closed - Opened by piotrszul over 3 years ago

#198 - add p-value calculation to HAIL implementation

Issue - State: closed - Opened by natwine almost 4 years ago

#197 - Grid Search for Parameter Optimisation

Issue - State: open - Opened by lm-fsng almost 4 years ago - 1 comment
Labels: enhancement

#196 - Release 0.10.2

Pull Request - State: closed - Opened by piotrszul almost 4 years ago

#195 - Improve release and versioning

Pull Request - State: closed - Opened by piotrszul almost 4 years ago

#194 - Improve release and versioning

Issue - State: closed - Opened by piotrszul almost 4 years ago - 1 comment
Labels: techdebt

#193 - Make the covariate calculation part of RF

Issue - State: closed - Opened by BauerLab almost 4 years ago - 3 comments
Labels: enhancement

#192 - Update the Cloud Marketplace example Notebooks to include logistic regression covariates

Issue - State: open - Opened by BauerLab almost 4 years ago - 1 comment
Labels: critical enhancement

#191 - Additional support for prediction

Issue - State: open - Opened by piotrszul almost 4 years ago - 1 comment

#190 - Add prediction command in cli.

Pull Request - State: closed - Opened by piotrszul almost 4 years ago

#189 - Align python formatting with InteliJ and remove python2 support.

Pull Request - State: closed - Opened by piotrszul almost 4 years ago

#188 - Align python code formatting between pylind and inteliJ

Issue - State: closed - Opened by piotrszul about 4 years ago
Labels: techdebt

#187 - Make pull request to hail with jar config changes.

Issue - State: closed - Opened by piotrszul about 4 years ago
Labels: techdebt

#186 - Update hail version to 0.2.61

Pull Request - State: closed - Opened by piotrszul about 4 years ago

#185 - Align code style checks with IntelJ fomatting

Issue - State: closed - Opened by piotrszul about 4 years ago
Labels: techdebt

#184 - Migrate CI to Github Actions

Pull Request - State: closed - Opened by piotrszul about 4 years ago

#183 - Migrate CI to Github Actions

Issue - State: closed - Opened by piotrszul about 4 years ago

#182 - Release v0.3.0

Pull Request - State: closed - Opened by piotrszul about 4 years ago

#181 - Added version into to cmd line and hail python.

Pull Request - State: closed - Opened by piotrszul about 4 years ago

#180 - Add version information to command line and python interfaces

Issue - State: closed - Opened by piotrszul about 4 years ago

#179 - Remove incomplete docs contents.

Pull Request - State: closed - Opened by piotrszul about 4 years ago

#178 - Trim the documentation

Issue - State: closed - Opened by piotrszul about 4 years ago

#177 - Cleanup readthedocs setup.

Pull Request - State: closed - Opened by piotrszul about 4 years ago

#176 - Fix hail package documentation at read the docs.

Issue - State: closed - Opened by piotrszul about 4 years ago

#175 - Updated pydocs for hail integration

Pull Request - State: closed - Opened by piotrszul about 4 years ago

#174 - Added a simple mode based imputation in python hail interface.

Pull Request - State: closed - Opened by piotrszul about 4 years ago

#173 - Update/write python docs for hail interface

Issue - State: closed - Opened by piotrszul about 4 years ago

#172 - Update documentation and notebooks for version 0.3

Pull Request - State: closed - Opened by piotrszul about 4 years ago

#171 - Update documentation and examples for 0.3 release.

Issue - State: closed - Opened by piotrszul about 4 years ago

#170 - Error when loading json model

Issue - State: closed - Opened by BMJHayward about 4 years ago - 1 comment

#169 - 168 Train rf cmd

Pull Request - State: open - Opened by BMJHayward over 4 years ago

#168 - Separate training command

Issue - State: open - Opened by BMJHayward over 4 years ago

#167 - 140 Predict cmd in CLI

Pull Request - State: closed - Opened by BMJHayward over 4 years ago

#166 - Bump junit from 4.12 to 4.13.1

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago
Labels: dependencies, java

#165 - Clustering sample

Issue - State: closed - Opened by TaniaCuppens over 4 years ago - 2 comments
Labels: help wanted

#164 - uncalled genotype issue

Issue - State: closed - Opened by ArashBayatDev over 4 years ago - 1 comment

#162 - #160 Web Visualiser

Pull Request - State: closed - Opened by ArashBayatDev over 4 years ago

#161 - num Case/Control in JSON model file

Issue - State: closed - Opened by ArashBayatDev over 4 years ago - 2 comments

#160 - Visualize Trees

Issue - State: closed - Opened by ArashBayatDev over 4 years ago - 1 comment

#159 - #158 Aws Marketplace

Pull Request - State: closed - Opened by ArashBayatDev over 4 years ago

#157 - #156 JsonRfAnalyser (Command Line Tree View)

Pull Request - State: closed - Opened by ArashBayatDev over 4 years ago

#156 - Tree View of the output JSON RandomForest model.

Issue - State: closed - Opened by ArashBayatDev over 4 years ago - 1 comment

#155 - Variable mTry at each node

Issue - State: open - Opened by ArashBayatDev over 4 years ago - 1 comment
Labels: enhancement

#154 - Variable training parameter

Issue - State: closed - Opened by ArashBayatDev over 4 years ago - 1 comment

#153 - Metadata in model files

Issue - State: open - Opened by ArashBayatDev over 4 years ago

#152 - Report Training process in Hail interface

Issue - State: closed - Opened by ArashBayatDev over 4 years ago

#151 - Merge Multiple RandomForest Model Files

Issue - State: open - Opened by ArashBayatDev over 4 years ago

#150 - RandomForest Model Java <-> R

Issue - State: closed - Opened by ArashBayatDev over 4 years ago - 1 comment

#149 - RandomForest Model Java <-> JSON

Issue - State: open - Opened by ArashBayatDev over 4 years ago - 1 comment

#148 - Decouple Training and Association

Issue - State: closed - Opened by ArashBayatDev over 4 years ago - 1 comment

#145 - #143 Add scalastyle and fix InteliJ warnings

Pull Request - State: closed - Opened by piotrszul almost 5 years ago

#142 - [#141] Format code with scalafmr

Pull Request - State: closed - Opened by piotrszul almost 5 years ago

#140 - Predict Labels with VariantSpark

Issue - State: closed - Opened by ArashBayatDev almost 5 years ago - 8 comments

#139 - Handling missing genotype calls

Issue - State: closed - Opened by schonbej almost 5 years ago - 1 comment

#138 - #137 Adds support for GRCh38 genome reference

Pull Request - State: closed - Opened by piotrszul almost 5 years ago

#137 - GRCh38 reference genome with Hail based Variant Spark

Issue - State: closed - Opened by schonbej almost 5 years ago - 2 comments