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Katsevich-Lab
/
sceptre
An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.
https://katsevich-lab.github.io/sceptre/
GNU General Public License v3.0
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Make the links on the webpage to the e-book open new tabs
#82
ekatsevi
opened
10 months ago
0
Update the sentence “support for Parse Biosciences outputs is coming soon” in the vignette
#81
ekatsevi
closed
8 months ago
2
Change `fit_parametric_curve` argument to `resampling_approximation`
#80
ekatsevi
closed
7 months ago
2
Look into the `user_specified_covariates` field of the `sceptre_object`. Are we still using this? If not, discard.
#79
ekatsevi
closed
9 months ago
1
Make `discovery_pairs` an optional argument to `set_analysis_parameters()` and fix bug related to `discovery_pairs` and calibration check
#78
ekatsevi
closed
8 months ago
0
Flesh out man pages for exported functions
#77
ekatsevi
closed
7 months ago
0
Separate data into separate package
#76
ekatsevi
closed
7 months ago
0
Create a report regarding test coverage
#75
ekatsevi
closed
8 months ago
0
Check that passed arguments are of the correct types
#74
ekatsevi
opened
10 months ago
0
Fix bug in log-transformed scales
#73
ekatsevi
closed
9 months ago
1
Plotting Response Expression for a Given Target vs. Unperturbed/Control Cells
#72
ale-gomez
closed
10 months ago
7
fit_parametric_curve = FALSE and failure issue
#71
redbybeing
closed
10 months ago
16
Control cell definition
#70
redbybeing
closed
11 months ago
3
Dev
#69
timothy-barry
closed
11 months ago
0
Running sceptre 0.9.1 several questions
#68
redbybeing
closed
11 months ago
16
Unsure about 'p_value' and 'significant' columns on results_run_discovery_analysis output dataframe
#67
ale-gomez
closed
11 months ago
2
singleton strategy can not be used
#66
UronicAcid
closed
1 year ago
1
Further accelerate the `plot_assign_grnas()` function
#65
timothy-barry
closed
1 year ago
1
add test_file
#64
timothy-barry
closed
1 year ago
0
object '_sceptre_threshold_count_matrix' not found
#63
yaxiliu-1996
closed
11 months ago
11
Update/unit testing
#61
jdeu1023
closed
1 year ago
0
Update/unit testing
#60
jdeu1023
closed
1 year ago
0
CRISPRi design considerations for using SCEPTRE-LR low moi
#59
pipes82
closed
1 year ago
5
Update to `testthat` 3e
#58
jdeu1023
closed
1 year ago
0
`plot_cell_covariates`
#57
timothy-barry
closed
1 year ago
1
Fleshing out `return_cis_pairs`
#56
timothy-barry
closed
1 year ago
1
Add parallel functionality for Windows
#55
jdeu1023
opened
1 year ago
0
Update plot grna count distributions
#54
jdeu1023
closed
1 year ago
8
Try to find bugs/errors using the low- and high-MOI example data.
#53
jdeu1023
closed
1 year ago
2
Create a violin plot to illustrate the expression of a gene across treatment and control groups for a given perturbation; add a sceptre p-value as a star
#52
jdeu1023
closed
1 year ago
0
Write a unit test to check `n_nonzero_trt`
#51
jdeu1023
closed
1 year ago
0
Downsampling in calibration and discovery QQ plots
#50
jdeu1023
closed
1 year ago
2
Update plot_assign_grnas with downsampling and legends
#49
jdeu1023
closed
1 year ago
0
Update plot_grna_count_distribution bins
#48
jdeu1023
closed
1 year ago
0
add downsampling and legend to plot_assign_grnas
#47
jdeu1023
closed
1 year ago
0
update plot_run_power_analysis and add to sceptre_object print method
#46
jdeu1023
closed
1 year ago
1
add plot_run_power_check for plotting positive control p-values
#45
jdeu1023
closed
1 year ago
1
Write a function to visualize gRNA count distributions across cells
#44
ekatsevi
closed
1 year ago
1
Write a function to visualize positive control results
#43
ekatsevi
closed
1 year ago
1
Error in set(x, j = name, value = value) : Supplied 2 items to be assigned to 1355970 items of column 'formula'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code. Calls: $<- -> $<-.data.table -> set
#42
redbybeing
closed
1 year ago
12
Two or more non-targeting gRNAs must be present when running a calibration check.
#41
redbybeing
closed
1 year ago
2
could not find function "run_sceptre_highmoi_experimental"
#40
redbybeing
closed
1 year ago
3
Covariates to include in new high-moi
#39
redbybeing
closed
1 year ago
5
Definition of control cells
#38
redbybeing
closed
1 year ago
3
Question about negative/positive controls
#37
nchernia
closed
1 year ago
8
Is faster version high-moi sceptre out yet?
#36
redbybeing
closed
1 year ago
11
gRNA-to cell in SCEPTRE lowMOI
#35
glettre
closed
1 year ago
3
Question about full output
#34
nchernia
closed
1 year ago
1
High MOI combine_perturbations function error
#33
redbybeing
closed
1 year ago
2
High MOI when there's multiple guides targeting one gene
#32
redbybeing
closed
1 year ago
2
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