HallLab/clarite-python issues and pull requests

#124 - Open Betas

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

#123 - Warning (Flake8 E721)

Issue - State: closed - Opened by AndreRico 11 months ago
Labels: enhancement, good first issue

#122 - Return from the interaction_study() function

Issue - State: closed - Opened by AndreRico 11 months ago - 1 comment

#121 - Return Converged with LRT-Pvalue NaN

Issue - State: closed - Opened by AndreRicoPSU almost 1 year ago - 2 comments

#120 - SettingWithCopyWarning on Regression runs

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

#119 - Regressions with Error after Multiprocessing release python > 3.8

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

#118 - Function self.get_weights(regression_variable) return None

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

#117 - Error type variable on Weight Regression with Clusters

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

#116 - Regression matrix with empty categories.

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

#115 - GLM Regression code classification for control and case

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

#114 - Add Multiple Outcome Capability to clarite.plot.top_results function

Issue - State: open - Opened by nep63 over 2 years ago

#113 - Improve memory usage and logging info by moving the encoding step

Pull Request - State: closed - Opened by jrm5100 about 3 years ago - 1 comment

#112 - Add multiprocessing

Pull Request - State: closed - Opened by jrm5100 about 3 years ago
Labels: enhancement

#111 - Change "weighted" to "edge" and fix docs

Pull Request - State: closed - Opened by jrm5100 about 3 years ago

#110 - Resize images in README

Pull Request - State: closed - Opened by jrm5100 about 3 years ago

#109 - Version 2

Pull Request - State: closed - Opened by jrm5100 about 3 years ago - 1 comment

#108 - Potentially useful library: Samplics

Issue - State: open - Opened by jrm5100 over 3 years ago
Labels: hmm

#107 - Fix error when the min_n filter fails

Pull Request - State: closed - Opened by jrm5100 over 3 years ago - 1 comment
Labels: bug

#106 - Poetry config update

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#105 - Update release notes

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#104 - Switch to Poetry

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#103 - Revert "Switch to Poetry, and update test data with some rounded valu…

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#102 - Switch to Poetry

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#101 - 100 standardize data

Pull Request - State: closed - Opened by jrm5100 over 3 years ago
Labels: enhancement

#100 - Report standardized betas

Issue - State: closed - Opened by jrm5100 over 3 years ago - 1 comment
Labels: enhancement

#99 - EWAS only sometimes raises an error when outcome NAs are not removed

Issue - State: closed - Opened by tomszar over 3 years ago - 2 comments

#98 - Issue#97 - Adding an option to report betas for individual categories

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#97 - Add `report_betas` option to EWAS functions

Issue - State: closed - Opened by jrm5100 over 3 years ago - 1 comment
Labels: enhancement

#96 - Update README.rst

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#95 - Fix outlier removal

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#94 - fix #93

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#93 - modify.remove_outliers only prints results, doesn't remove them

Issue - State: closed - Opened by jrm5100 over 3 years ago

#92 - Improve compatibility with symbol-laden variable names

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#91 - 90 encode var names

Pull Request - State: closed - Opened by jrm5100 over 3 years ago - 1 comment

#90 - Automatically fix and un-fix variable names

Issue - State: closed - Opened by jrm5100 over 3 years ago
Labels: enhancement

#89 - Minor doc fixes and install fix for R code

Pull Request - State: closed - Opened by jrm5100 over 3 years ago

#88 - added return_figure option to manhattan plot

Pull Request - State: closed - Opened by tomszar over 3 years ago
Labels: enhancement

#87 - Add return axes option to plots

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

#86 - Update ewas_r.R

Pull Request - State: closed - Opened by jrm5100 almost 4 years ago - 1 comment

#85 - Add survey weights to interaction tests

Issue - State: open - Opened by jrm5100 almost 4 years ago

#84 - Interaction improvements

Pull Request - State: closed - Opened by jrm5100 almost 4 years ago - 1 comment

#83 - Update CLI and add tests

Issue - State: open - Opened by jrm5100 almost 4 years ago
Labels: bug, tests, low priority

#82 - 77 plot labels

Pull Request - State: closed - Opened by jrm5100 almost 4 years ago - 1 comment

#81 - GitHub actions

Pull Request - State: closed - Opened by jrm5100 almost 4 years ago

#80 - Add main effects interactions

Pull Request - State: closed - Opened by jrm5100 almost 4 years ago

#79 - Interactions need main effects as well

Issue - State: closed - Opened by jrm5100 almost 4 years ago

#78 - 76 interactions

Pull Request - State: closed - Opened by jrm5100 almost 4 years ago
Labels: enhancement

#77 - Fix top_n labels so that they aren't repeated when multiple phenotypes are present

Issue - State: closed - Opened by jrm5100 almost 4 years ago
Labels: bug

#76 - Interaction

Issue - State: closed - Opened by jrm5100 almost 4 years ago - 1 comment
Labels: enhancement, hmm

#75 - Changes made in R, Python, and R tests

Pull Request - State: closed - Opened by jrm5100 almost 4 years ago

#74 - Enforce using the same data rows in each model for weighted categorical LRT tests

Issue - State: closed - Opened by jrm5100 almost 4 years ago
Labels: enhancement, documentation

#73 - 70 survey subset

Pull Request - State: closed - Opened by jrm5100 about 4 years ago

#72 - Update docs

Pull Request - State: closed - Opened by jrm5100 over 4 years ago
Labels: documentation

#71 - Update Survey Design docs

Issue - State: closed - Opened by jrm5100 over 4 years ago
Labels: documentation

#70 - Better handle survey subsets

Issue - State: closed - Opened by jrm5100 over 4 years ago - 6 comments
Labels: enhancement

#69 - Add modify.normalization

Issue - State: open - Opened by jrm5100 over 4 years ago
Labels: enhancement

#68 - 1.0.1 Release

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#67 - Merge fork into develop

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#66 - Miscellaneous fixes for v1.0.1

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#65 - Update instructions for configuring R

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#64 - 61 improve top results plot

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#63 - 60 ewas r errors

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#62 - The skew calculation of the distribution plot reports NaN

Issue - State: closed - Opened by jrm5100 over 4 years ago - 1 comment

#61 - Improve top_results plot

Issue - State: closed - Opened by jrm5100 over 4 years ago

#60 - Errors running ewas_r

Issue - State: closed - Opened by jrm5100 over 4 years ago - 1 comment

#59 - Allow a Series in some functions and strictly require a DataFrame in others

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#58 - Add the parameter to SurveyDesignSpec and use it

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#57 - 46 new plot

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#56 - Add the skewness function, update the CLI, and add tests

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#55 - Add a function to help with missing weights

Issue - State: closed - Opened by jrm5100 over 4 years ago

#54 - Fix some tests and improve logging around missing values

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#53 - Add a 'skewness' function to 'describe'

Issue - State: closed - Opened by jrm5100 over 4 years ago

#52 - Tests and Improvements

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#51 - Review ewas test results

Issue - State: closed - Opened by jrm5100 over 4 years ago - 2 comments

#50 - Improve ease-of-use with R

Pull Request - State: closed - Opened by jrm5100 over 4 years ago - 1 comment

#49 - 38 regression object refactor

Pull Request - State: closed - Opened by jrm5100 over 4 years ago - 1 comment

#48 - Set up Conda installation method

Issue - State: open - Opened by jrm5100 over 4 years ago
Labels: enhancement

#47 - Fix warning in remove extra categories

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#46 - New Plot: Top results with pvalue and beta values

Issue - State: closed - Opened by jrm5100 over 4 years ago - 1 comment

#45 - 44 manhattan plot

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#44 - Update Manhattan Plot function(s)

Issue - State: closed - Opened by jrm5100 over 4 years ago

#43 - Add custom test number for correcting pvalues

Issue - State: closed - Opened by jrm5100 over 4 years ago - 2 comments
Labels: wontfix

#42 - 41 categorize bug

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#41 - `categorize` has trouble when attempting to classify a string variable as continuous

Issue - State: closed - Opened by jrm5100 over 4 years ago

#40 - Add drop_extra_categories CLI and update docs

Pull Request - State: closed - Opened by jrm5100 over 4 years ago

#39 - 37 empty cats

Pull Request - State: closed - Opened by jrm5100 over 4 years ago - 1 comment
Labels: bug

#38 - Reorganize Regression object

Issue - State: closed - Opened by jrm5100 over 4 years ago - 1 comment

#37 - EWAS: Categories with no occurrences result in a Singular Matrix error.

Issue - State: closed - Opened by jrm5100 over 4 years ago - 1 comment

#36 - Improve compatibility with Series

Issue - State: closed - Opened by jrm5100 over 4 years ago

#35 - Add NaN warnings to some functions

Issue - State: open - Opened by jrm5100 over 4 years ago
Labels: enhancement

#34 - Limit Pandas version to < 1 or ensure compatibility with Pandas 1.0+

Issue - State: closed - Opened by jrm5100 over 4 years ago

#33 - Support an 'ax' argument for clarite.plot.histogram

Issue - State: closed - Opened by jrm5100 over 4 years ago - 1 comment

#32 - clarite.modify.merge_variables fails when used with a series

Issue - State: closed - Opened by jrm5100 over 4 years ago - 1 comment

#31 - Support Multinominal Regression for Categorical Phenotypes

Issue - State: open - Opened by jrm5100 over 4 years ago
Labels: enhancement

#30 - Update README and add citations

Pull Request - State: closed - Opened by jrm5100 almost 5 years ago

#29 - Add a citation page to the docs

Pull Request - State: closed - Opened by jrm5100 almost 5 years ago

#28 - Make phenome-wide EWAS easier

Issue - State: closed - Opened by jrm5100 almost 5 years ago - 1 comment
Labels: hmm

#27 - 22 custom threshold manhattan

Pull Request - State: closed - Opened by jrm5100 almost 5 years ago
Labels: enhancement

#26 - add redirect files

Pull Request - State: closed - Opened by jrm5100 almost 5 years ago

#25 - Initial attempt

Pull Request - State: closed - Opened by jrm5100 almost 5 years ago

GitHub / HallLab/clarite-python issues and pull requests