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noamteyssier
/
crispr_screen
Efficient Differential Expression and Gene Aggregation for CRISPR screens.
https://noamteyssier.github.io/crispr_screen/
MIT License
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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
0
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
0
chore: update semver
#160
noamteyssier
closed
4 days ago
1
install dependabot
#159
noamteyssier
closed
4 days ago
0
chore: update geopagg version and project semver
#158
noamteyssier
closed
4 days ago
1
update geopagg which enforces monotonocity in empirical FDR
#157
noamteyssier
closed
4 days ago
0
create a new submodule to resample control libraries
#156
noamteyssier
closed
23 hours ago
0
154 use z score threshold in geopagg
#155
noamteyssier
closed
5 days ago
0
use z-score threshold in geopagg
#154
noamteyssier
closed
5 days ago
0
Development
#153
noamteyssier
closed
5 days ago
0
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
0
feat: added cli option to use all sgRNAs instead of just non-targetin…
#148
noamteyssier
closed
2 weeks ago
0
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
0
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
1
implement the geopagg algorithm
#140
noamteyssier
closed
1 month ago
1
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
0
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
0
Catch empty / NaN values in matrix
#125
noamteyssier
closed
6 months ago
0
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
0
121 report the null log2fc standard deviation in results
#122
noamteyssier
closed
1 year ago
0
report the null log2fc standard deviation in results
#121
noamteyssier
closed
1 year ago
0
bump version + intc version
#120
noamteyssier
closed
1 year ago
0
fix intc bug with alternative
#119
noamteyssier
closed
1 year ago
0
117 update crispr screen to use newer intc algorithm
#118
noamteyssier
closed
1 year ago
0
update crispr_screen to use newer INTC algorithm
#117
noamteyssier
closed
1 year ago
0
write all output files to a directory
#116
noamteyssier
opened
1 year ago
0
114 update intc
#115
noamteyssier
closed
1 year ago
0
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