noamteyssier crispr_screen issues

noamteyssier / crispr_screen

Efficient Differential Expression and Gene Aggregation for CRISPR screens.

https://noamteyssier.github.io/crispr_screen/

MIT License

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issues

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163 set number of draws for each resampled control

#164 noamteyssier closed 21 hours ago
1
set number of draws for each resampled control

#163 noamteyssier closed 21 hours ago
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156 create a new submodule to resample control libraries

#162 noamteyssier closed 23 hours ago
1
rebase resample with main

#161 noamteyssier closed 1 day ago
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chore: update semver

#160 noamteyssier closed 4 days ago
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install dependabot

#159 noamteyssier closed 4 days ago
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chore: update geopagg version and project semver

#158 noamteyssier closed 4 days ago
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update geopagg which enforces monotonocity in empirical FDR

#157 noamteyssier closed 4 days ago
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create a new submodule to resample control libraries

#156 noamteyssier closed 23 hours ago
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154 use z score threshold in geopagg

#155 noamteyssier closed 5 days ago
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use z-score threshold in geopagg

#154 noamteyssier closed 5 days ago
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Development

#153 noamteyssier closed 5 days ago
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135 duplicated short arguments in clap

#152 noamteyssier closed 5 days ago
1
150 perform filtering based on basemean only in the controls

#151 noamteyssier closed 5 days ago
1
Perform filtering based on baseMean only in the controls

#150 noamteyssier closed 5 days ago
1
refactor: set minimum base mean to 100

#149 noamteyssier closed 2 weeks ago
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feat: added cli option to use all sgRNAs instead of just non-targetin…

#148 noamteyssier closed 2 weeks ago
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set option to use negative all genes in NTC draws for geopagg

#147 noamteyssier closed 2 weeks ago
1
144 introduce an option for weighted geometric mean on p values instead of count aggregation before da tests

#146 noamteyssier closed 2 weeks ago
0
set minimum base-mean threshold to 100

#145 noamteyssier closed 2 weeks ago
1
introduce an option for weighted geometric mean on p-values instead of count aggregation before DA tests

#144 noamteyssier closed 2 weeks ago
1
142 use polars as dataframe throughout make code clearer

#143 noamteyssier closed 4 weeks ago
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use polars as dataframe throughout make code clearer

#142 noamteyssier closed 2 weeks ago
1
140 implement the geopagg algorithm

#141 noamteyssier closed 1 month ago
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implement the geopagg algorithm

#140 noamteyssier closed 1 month ago
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introduce a top 3 heuristic when performing tests

#139 noamteyssier opened 2 months ago
1
report the false gene groupings for RRA and INC

#138 noamteyssier opened 2 months ago
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136 issue with seeding and rngs 1

#137 noamteyssier closed 2 months ago
1
issue with seeding and RNGs

#136 noamteyssier closed 2 months ago
1
duplicated short arguments in clap

#135 noamteyssier closed 5 days ago
2
Visualisation

#134 nangosyah closed 2 months ago
1
132 set parameterized minimum threshold for performing differential abundance testing

#133 noamteyssier closed 5 months ago
1
set parameterized minimum threshold for performing differential abundance testing

#132 noamteyssier closed 5 months ago
0
check for P1/P2 transcription start site in name and warn users to generate a table that separates them

#131 noamteyssier opened 6 months ago
0
126 make regex available for treatment and control sample name inputs

#130 noamteyssier closed 6 months ago
1
127 check that ntc tokens actually exist when running inc

#129 noamteyssier closed 6 months ago
1
125 catch empty nan values in matrix

#128 noamteyssier closed 6 months ago
1
Check that NTC-tokens actually exist when running INC

#127 noamteyssier closed 6 months ago
0
Make regex available for treatment and control sample name inputs

#126 noamteyssier closed 6 months ago
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Catch empty / NaN values in matrix

#125 noamteyssier closed 6 months ago
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123 introduce test and agg as separate subcommands

#124 noamteyssier closed 7 months ago
1
introduce test and agg as separate subcommands

#123 noamteyssier closed 7 months ago
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121 report the null log2fc standard deviation in results

#122 noamteyssier closed 1 year ago
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report the null log2fc standard deviation in results

#121 noamteyssier closed 1 year ago
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bump version + intc version

#120 noamteyssier closed 1 year ago
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fix intc bug with alternative

#119 noamteyssier closed 1 year ago
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117 update crispr screen to use newer intc algorithm

#118 noamteyssier closed 1 year ago
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update crispr_screen to use newer INTC algorithm

#117 noamteyssier closed 1 year ago
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write all output files to a directory

#116 noamteyssier opened 1 year ago
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114 update intc

#115 noamteyssier closed 1 year ago
0