v0.10.1

Minor updates to v0.10.0. A new gene position data frame gene_position_data_frame_grch37 is added.

v0.10.0

sceptre 0.10.0 (2024-04-02)

Version 0.10.0 is a major update to the sceptre package. This version provides support for the analysis of large-scale single-cell CRISPR screen data. It also includes several other, minor updates.

• We have introduced the ondisc-backed sceptre_object, which is a special kind of sceptre_object in which the data are stored on-disk as opposed to in-memory.

• We have made the sceptre R package compatible with the sceptre Nextflow pipeline.

• We have added the function plot_response_grna_target_pair(), which creates a violin plot of the expression level of a specified gene across treatment and control groups of a specified target.

• We have added the function get_grna_assignments(), which facilitates obtaining the gRNA-to-cell assignments.

• We have updated the sceptre e-book, adding two new parts: a part on at-scale sceptre and a part on the methodology underlying sceptre.

• We have made the discovery pairs data frame and the positive control pairs data frame optional arguments to the set_analysis_parameters() function.

• We have added a comprehensive suite of unit tests to help verify correctness of the code.

• We have fleshed out the man pages, for example by adding a runable example to each.

• We have moved the example data within the sceptre package into the companion sceptredata package.

• We have issued minor bug fixes.

Please note that v0.10.0 is a higher version number than v0.9.2.

v0.9.2

Four updates.

1. Add an n_processors argument to the functions that enable parallelization to allow users to select the number of processors to use. (The default, n_processors = "auto", selects the number of processors to use based on the number of processors available on the machine.)
2. Add a log_dir argument enabling users to specify the directory in which to write the log files.
3. Accelerate the plot_assign_grnas function.
4. Fix the functionality for identifying mitochondrial genes; now, genes prefixed by "MT-" or "mt-" are considered mitochondrial.

v0.9.1

• New import_from_parse() experimental function.
• Added support for "bonferroni" gRNA integration strategy.

v0.9.0

v0.9.0 is a substantial upgrade to the package (see changelog for details).