noamteyssier/crispr_screen issues and pull requests

#180 - Update bon requirement from 2.3.0 to 3.3.2

Pull Request - State: open - Opened by dependabot[bot] about 1 month ago
Labels: dependencies

#179 - Update bon requirement from 2.3.0 to 3.3.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago - 1 comment
Labels: dependencies

#178 - Update statrs requirement from 0.17.1 to 0.18.0

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

#177 - Update polars requirement from 0.43.1 to 0.45.1

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

#176 - Update bon requirement from 2.3.0 to 3.3.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago - 1 comment
Labels: dependencies

#175 - Update bon requirement from 2.3.0 to 3.2.0

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: dependencies

#174 - Update bon requirement from 2.3.0 to 3.1.0

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: dependencies

#173 - Update bon requirement from 2.3.0 to 3.0.1

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#172 - Update polars requirement from 0.43.1 to 0.44.2

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#171 - 170 set minimum fdr in sgrna to the minimum nonzero value

Pull Request - State: closed - Opened by noamteyssier 3 months ago - 1 comment

#170 - set minimum fdr in sgRNA to the minimum nonzero value

Issue - State: closed - Opened by noamteyssier 3 months ago
Labels: error-handling

#169 - Update polars requirement from 0.43.1 to 0.44.0

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#168 - include number of significant sgRNAs as an output column in gene results

Issue - State: open - Opened by noamteyssier 4 months ago
Labels: enhancement

#167 - 166 geopagg bug with gene superstring inclusion

Pull Request - State: closed - Opened by noamteyssier 4 months ago - 1 comment

#166 - geopagg bug with gene superstring inclusion

Issue - State: closed - Opened by noamteyssier 4 months ago
Labels: bug

#165 - Update polars requirement from 0.42.0 to 0.43.1

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#164 - 163 set number of draws for each resampled control

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

#163 - set number of draws for each resampled control

Issue - State: closed - Opened by noamteyssier 5 months ago
Labels: resample

#162 - 156 create a new submodule to resample control libraries

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

#161 - rebase resample with main

Pull Request - State: closed - Opened by noamteyssier 5 months ago

#160 - chore: update semver

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

#159 - install dependabot

Issue - State: closed - Opened by noamteyssier 5 months ago
Labels: development

#158 - chore: update geopagg version and project semver

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

#157 - update geopagg which enforces monotonocity in empirical FDR

Issue - State: closed - Opened by noamteyssier 5 months ago
Labels: bug

#156 - create a new submodule to resample control libraries

Issue - State: closed - Opened by noamteyssier 5 months ago
Labels: algorithm

#155 - 154 use z score threshold in geopagg

Pull Request - State: closed - Opened by noamteyssier 5 months ago

#154 - use z-score threshold in geopagg

Issue - State: closed - Opened by noamteyssier 5 months ago

#153 - Development

Pull Request - State: closed - Opened by noamteyssier 5 months ago

#152 - 135 duplicated short arguments in clap

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

#151 - 150 perform filtering based on basemean only in the controls

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

#150 - Perform filtering based on baseMean only in the controls

Issue - State: closed - Opened by noamteyssier 5 months ago - 1 comment
Labels: algorithm

#149 - refactor: set minimum base mean to 100

Pull Request - State: closed - Opened by noamteyssier 5 months ago

#148 - feat: added cli option to use all sgRNAs instead of just non-targetin…

Pull Request - State: closed - Opened by noamteyssier 5 months ago

#147 - set option to use negative all genes in NTC draws for geopagg

Issue - State: closed - Opened by noamteyssier 5 months ago - 1 comment
Labels: enhancement

#146 - 144 introduce an option for weighted geometric mean on p values instead of count aggregation before da tests

Pull Request - State: closed - Opened by noamteyssier 5 months ago

#145 - set minimum base-mean threshold to 100

Issue - State: closed - Opened by noamteyssier 6 months ago - 1 comment
Labels: enhancement

#144 - introduce an option for weighted geometric mean on p-values instead of count aggregation before DA tests

Issue - State: closed - Opened by noamteyssier 6 months ago - 1 comment
Labels: enhancement, algorithm, development

#143 - 142 use polars as dataframe throughout make code clearer

Pull Request - State: closed - Opened by noamteyssier 6 months ago

#142 - use polars as dataframe throughout make code clearer

Issue - State: closed - Opened by noamteyssier 6 months ago - 1 comment
Labels: development

#141 - 140 implement the geopagg algorithm

Pull Request - State: closed - Opened by noamteyssier 6 months ago - 1 comment

#140 - implement the geopagg algorithm

Issue - State: closed - Opened by noamteyssier 6 months ago - 1 comment
Labels: enhancement, algorithm

#139 - introduce a top 3 heuristic when performing tests

Issue - State: open - Opened by noamteyssier 7 months ago - 1 comment
Labels: enhancement, algorithm

#138 - report the false gene groupings for RRA and INC

Issue - State: open - Opened by noamteyssier 7 months ago
Labels: enhancement

#137 - 136 issue with seeding and rngs 1

Pull Request - State: closed - Opened by noamteyssier 7 months ago - 1 comment

#136 - issue with seeding and RNGs

Issue - State: closed - Opened by noamteyssier 7 months ago - 1 comment
Labels: bug

#135 - duplicated short arguments in clap

Issue - State: closed - Opened by noamteyssier 9 months ago - 2 comments
Labels: bug

#134 - Visualisation

Issue - State: closed - Opened by nangosyah 10 months ago - 1 comment

#133 - 132 set parameterized minimum threshold for performing differential abundance testing

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

#132 - set parameterized minimum threshold for performing differential abundance testing

Issue - State: closed - Opened by noamteyssier 11 months ago
Labels: enhancement

#131 - check for P1/P2 transcription start site in name and warn users to generate a table that separates them

Issue - State: open - Opened by noamteyssier 11 months ago
Labels: enhancement

#130 - 126 make regex available for treatment and control sample name inputs

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

#129 - 127 check that ntc tokens actually exist when running inc

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

#128 - 125 catch empty nan values in matrix

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

#127 - Check that NTC-tokens actually exist when running INC

Issue - State: closed - Opened by noamteyssier 12 months ago
Labels: bug

#126 - Make regex available for treatment and control sample name inputs

Issue - State: closed - Opened by noamteyssier 12 months ago
Labels: enhancement

#125 - Catch empty / NaN values in matrix

Issue - State: closed - Opened by noamteyssier 12 months ago
Labels: bug

#124 - 123 introduce test and agg as separate subcommands

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