Katsevich-Lab sceptre issues

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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issues

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Run gRNA assignment error

#157 nhu-github closed 1 week ago
2
No negative control pair passes pairwise QC.

#154 AAAAAbetter closed 1 month ago
0
non-targeting gRNAs

#151 nhu-github closed 1 month ago
1
NonZero assignment

#149 jpulecio closed 1 month ago
0
subscript out of bonds

#147 kasperdanielhansen closed 1 month ago
2
Check and fix multicollinearity for association analysis and gRNA assignment

#146 nhu-github opened 2 months ago
7
gene_position_data_frame contains Ensembl id's, is it possible to add gene names

#143 Saranya-Balachandran closed 2 months ago
0
Data without gRNA UMI count matrix

#141 Larrycpan closed 2 months ago
1
The difference between sceptre or seurat Mixscape?

#139 xiasijian closed 3 months ago
3
Add feature that automatically removes nested categorical covariates

#138 ekatsevi opened 3 months ago
0
Error in eigen(Zt_wZ, symmetric = TRUE)

#135 Yuanca9 opened 4 months ago
4
Allow users to specify their own gRNA assignments rather than having sceptre compute them

#133 ekatsevi opened 4 months ago
0
Add feature to track version of sceptre used to create sceptre object

#132 ekatsevi opened 4 months ago
0
Error: C stack usage is too close to the limit

#130 vkartha closed 3 months ago
4
Please consider using parallelly::availableCores() instead of parallel::detectCores()

#128 HenrikBengtsson opened 5 months ago
2
Add module for computing the top k PCs of the response matrix and adding the PCs as covariates.

#125 timothy-barry opened 6 months ago
0
Regenerate example high-MOI data using ref genome 37; update book to use ref genome 37 in `construct_cis_pairs()`

#124 timothy-barry opened 6 months ago
0
Bug report from Veronica

#123 timothy-barry closed 6 months ago
3
Getting an errror when running the example code in "The Whole Game"

#119 jamesgalante closed 6 months ago
3
Fix the gene position data frame in the high-MOI example

#115 timothy-barry opened 6 months ago
0
Error in convert_covariate_df_to_design_matrix(covariate_data_frame = sceptre_object@covariate_data_frame, : The `formula_object` contains redundant information. This often occurs when one variable is `nested` inside another. For example, if the data frame contains a column `lane` with levels `lane_1`, `lane_2`, `lane_3`, and `lane_4` and a column `batch` with levels `batch_1` and `batch_2`, and if `lane_1` and `lane_2` are contained entirely within `batch_1` while `lane_3` and `lane_4` are contained entirely within `batch`2`, then `batch` is redundant. In this case `batch` should be removed from the formula object.

#114 redbybeing closed 6 months ago
5
Vanilla score test

#113 ekatsevi opened 7 months ago
1
Add more caching

#112 ekatsevi opened 7 months ago
1
Option to add cells with 0 counts for the target in run_qc()

#110 redbybeing closed 6 months ago
1
R kernel corruption when running run_calibration_check()

#109 zhaoshuoxp closed 7 months ago
7
could not find function "compute_genes_within_distance"

#108 redbybeing closed 7 months ago
20
print(sceptre_object) not working in ver10 for object created in previous ver

#107 redbybeing closed 7 months ago
2
Why aren't the processed assigned grna indexes in the raw assigned grna indexes?

#105 jamesgalante closed 7 months ago
5
How to take unperturbed cells as control?

#104 Larrycpan closed 7 months ago
8
update all api unit tests for recent changes

#103 jdeu1023 closed 7 months ago
2
Add continuous integration and code coverage badge to github

#102 jdeu1023 opened 8 months ago
0
Fix C++ compiler warnings

#101 timothy-barry closed 8 months ago
0
Are the reported sceptre p-values adjusted?

#100 ejagoda14 closed 8 months ago
2
Consider improving the efficiency of negative control pair construction for high-MOI data out-of-core.

#99 timothy-barry opened 9 months ago
0
Consider adding functionality to import R matrices into ondisc format

#98 timothy-barry closed 8 months ago
0
Consider adding empirical FDR correction option (as a last resort for ameliorating miscalibration)

#97 timothy-barry closed 8 months ago
0
Document `ondisc` package

#96 timothy-barry closed 7 months ago
0
Improve handling of data in which gRNA vector information is supplied.

#95 timothy-barry closed 8 months ago
2
Write gRNA-to-cell assignment matrix to disk.

#94 timothy-barry closed 8 months ago
10
Consider adding special option for analyzing ~100+ million trans pairs.

#93 timothy-barry closed 8 months ago
0
Add simple optimizations (e.g., factors in the pairs to analyze df and/or results df, removing pieces from the sceptre_object) to reduce memory.

#92 timothy-barry closed 8 months ago
0
Handle the "vector" column in a more sophisticated way in the gRNA target data frame.

#91 timothy-barry closed 8 months ago
0
Unit tests for API functions

#90 jdeu1023 closed 8 months ago
0
Make sure every single gRNA is assigned to cells in low MOI.

#89 timothy-barry closed 9 months ago
1
Add option to apply absolute QC thresholds, rather than quantiles

#88 ekatsevi opened 9 months ago
0
Export gRNA assignments as sparse binary matrix

#87 ekatsevi closed 9 months ago
1
fixed issue with scales library update making plots weird

#86 jdeu1023 closed 9 months ago
1
Questions about grna integration options and grna assignment output

#85 ejagoda14 closed 9 months ago
7
Complete code to create individual pair plot

#84 ekatsevi closed 8 months ago
0
Add unit tests covering each API function at least once

#83 ekatsevi closed 8 months ago
0