Ecosyste.ms: Issues

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GitHub / noamteyssier/crispr_screen issues and pull requests

#80 - add testing on enrichment

Issue - State: closed - Opened by noamteyssier about 2 years ago
Labels: testing

#79 - 78 better documentation on help

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#78 - better documentation on help

Issue - State: closed - Opened by noamteyssier about 2 years ago
Labels: documentation

#77 - 65 add fold changes to gene results

Pull Request - State: closed - Opened by noamteyssier about 2 years ago - 1 comment

#76 - 75 increase testing coverage

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#75 - increase testing coverage

Issue - State: closed - Opened by noamteyssier about 2 years ago

#74 - 72 incorporate coverage metrics

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#73 - write documentation site with mdbook

Issue - State: closed - Opened by noamteyssier about 2 years ago

#72 - incorporate coverage metrics

Issue - State: closed - Opened by noamteyssier about 2 years ago

#71 - 70 linting and formatting

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#70 - linting and formatting

Issue - State: closed - Opened by noamteyssier about 2 years ago

#69 - 68 drop polars as a dependency

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#68 - drop polars as a dependency

Issue - State: closed - Opened by noamteyssier about 2 years ago

#67 - made weighted loss the default value

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#66 - add gene score to gene results

Issue - State: closed - Opened by noamteyssier about 2 years ago

#65 - add fold changes to gene results

Issue - State: closed - Opened by noamteyssier about 2 years ago

#64 - make wols the default

Issue - State: closed - Opened by noamteyssier about 2 years ago

#63 - move enrichment testing to statrs functions

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

#62 - 61 implement weighted least squares regression

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#61 - implement weighted least squares regression

Issue - State: closed - Opened by noamteyssier about 2 years ago
Labels: enhancement

#60 - 59 better approximate mageck with median instead of mean

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#59 - better approximate mageck with median instead of mean

Issue - State: closed - Opened by noamteyssier about 2 years ago

#58 - 57 variable alpha threshold

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#57 - variable alpha threshold

Issue - State: closed - Opened by noamteyssier about 2 years ago

#56 - 55 fix sgrna table printout with incorrect means

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#55 - fix sgrna table printout with incorrect means

Issue - State: closed - Opened by noamteyssier about 2 years ago

#54 - 53 hard switch to total normalization

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#53 - hard switch to total normalization

Issue - State: closed - Opened by noamteyssier about 2 years ago

#52 - fix fdr error for double zeros

Issue - State: closed - Opened by noamteyssier about 2 years ago

#51 - set bound on probability calculation

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#50 - fix bug on total normalization

Issue - State: closed - Opened by noamteyssier about 2 years ago

#49 - 48 include options in help descriptions

Pull Request - State: closed - Opened by noamteyssier about 2 years ago

#48 - include options in help descriptions

Issue - State: closed - Opened by noamteyssier about 2 years ago

#46 - fix bug where multiple controls and treatments cannot be provided as input

Issue - State: closed - Opened by noamteyssier about 2 years ago
Labels: bug

#44 - Spin out alpha-RRA into separate crate

Issue - State: closed - Opened by noamteyssier over 2 years ago - 1 comment
Labels: enhancement, development

#42 - optional multiple hypothesis correction

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: enhancement

#41 - implement truncated normal sgrna enrichment calculation

Issue - State: open - Opened by noamteyssier over 2 years ago
Labels: enhancement, algorithm

#39 - separate functions for sgrna and gene dataframe creation

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: development

#38 - 37 create sgrna result struct to clean up variable namespace

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

#37 - create sgrna result struct to clean up variable namespace

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: development

#36 - 19 implement benjamini hochberg false discovery rate correction

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

#35 - fix bug where < should be <= in empirical cdf

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

#34 - Explore weird asymptotic behavior with pvalues in RRA around 0.4

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: bug, question

#33 - confirm all pvalue arrays are sorted when passing into rra

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: bug

#32 - replace beta_inc with explicit beta cdf

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: bug

#31 - 30 return gene aggregation score in final results

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

#30 - return gene aggregation score in final results

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: enhancement

#29 - Aggregate all filtering functions into utils

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: development

#28 - 26 remove zero counts from rra calculation

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

#27 - 23 provide logging information with optional quiet argument

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

#26 - Remove zero counts from RRA calculation

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: enhancement, algorithm

#25 - Better error handling is control labels or treatment labes are not found in dataset

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: enhancement, error-handling

#24 - added a zscore filter on the logged ols calculation

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

#23 - Provide logging information with optional quiet argument

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: enhancement

#22 - Implement outlier detection removal before variance estimation

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: enhancement, algorithm

#21 - bug in compiling on MacOS

Issue - State: closed - Opened by noamteyssier over 2 years ago - 1 comment
Labels: bug

#20 - added readme

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

#19 - Implement benjamini-hochberg false discovery rate correction

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: enhancement, algorithm

#18 - Implement Z-Score Normalization Aggregation Method

Issue - State: open - Opened by noamteyssier over 2 years ago
Labels: enhancement, algorithm

#17 - Implement NTC-focused RRA

Issue - State: closed - Opened by noamteyssier over 2 years ago - 1 comment
Labels: enhancement, algorithm

#16 - Write up README

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: documentation

#15 - 14 linting throughout codebase to make more idiomatic

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

#9 - implement proper output handling

Issue - State: closed - Opened by noamteyssier over 2 years ago
Labels: enhancement