update website to reflect 0.9.1 changes

Katsevich-Lab · Oct 24, 2023 · f70e096 · f70e096
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sceptre
 Title: Analysis of Single-Cell CRISPR Screen Data
-Version: 0.9.0
+Version: 0.9.1
 Authors@R: 
     c(person(given = "Timothy",
            family = "Barry",

diff --git a/NEWS.html b/NEWS.html
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# sceptre 0.9.1 (2023-10-24)
+
+Version 0.9.1 is a minor update to version 0.9.0.
+
+-   We have added an experimental `import_data_from_parse()` function to import data from the output of Parse Biosciences CRISPR Detect.
+
+-   We have added support for the `"bonferroni"` gRNA integration strategy.
+
 # sceptre 0.9.0 (2023-10-20)
 
 Version 0.9.0 is a total rework of the `sceptre` package. The new version of the package has a fresh user interface and is faster, more memory-efficient, and more fully featured than previous versions. We summarize key updates here.

diff --git a/R/import_functs.R b/R/import_functs.R
@@ -220,7 +220,7 @@ write_sceptre_object_to_cellranger_format <- function(sceptre_object, directory)
 
 #' Import data from Parse (experimental)
 #'
-#' `import_data_from_parse()` imports data from the output of the Parse count matrix generation program. See \href{https://timothy-barry.github.io/sceptre-book/sceptre.html#sec-whole_game_import_data}{Section 1 of the introductory chapter in the manual} for more information about this function. It is assumed that the data are stored in a single set of files (as opposed to multiple sets of files corresponding to, e.g., different samples).
+#' `import_data_from_parse()` imports data from the output of the Parse count matrix generation program. See \href{https://timothy-barry.github.io/sceptre-book/import-data.html#import-from-the-parse-program-experimental}{Chapter 1 of the manual} for more information about this function. It is assumed that the data are stored in a single set of files (as opposed to multiple sets of files corresponding to, e.g., different samples).
 #'
 #' `import_data_from_parse()` is experimental, and the API of this function is subject to change. We expect the API to solidify as we learn more about the Parse platform and the structure of the Parse count matrix generation program output.
 #'

diff --git a/R/sceptre.R b/R/sceptre.R
@@ -2,7 +2,8 @@ utils::globalVariables(c("n_nonzero_trt", "n_nonzero_cntrl", "pair_str", "assign
                          "multiple_grnas", "x", "grna_id", "grna_expressions_bin", "bin_counts",
                          "significant", "lab", "p_values", "pass_qc", "fraction_cells_removed",
                          "grna_id", "pass_qc", "grna_group", "p_value", "gene_id", "response_id",
-                         "log_2_fold_change", "reject", "y", "grna_target", "gene_position_data_frame_grch38"))
+                         "log_2_fold_change", "reject", "y", "grna_target", "gene_position_data_frame_grch38",
+                         "any_pass_qc"))
 #' sceptre
 #'
 #' `sceptre` is an R package for single-cell CRISPR screen data analysis that emphasizes statistical rigor, computational efficiency, and ease of use.

diff --git a/README.Rmd b/README.Rmd
@@ -27,19 +27,19 @@ An R package for single-cell CRISPR screen data analysis, emphasizing statistica
 
 <!-- badges: end -->
 
-## Release of `sceptre` v0.9.0
+## Release of `sceptre` v0.9.1
 
-We are excited to announce the release of `sceptre` v0.9.0, a substantial update to the package. This milestone includes the following developments:
+We are excited to announce the release of `sceptre` v0.9.1, a substantial update to the package. This milestone includes the following developments:
 
 -   A reimagined user experience based on a modular, object-oriented workflow.
 -   Further improvements in speed and memory efficiency.
 -   A unified interface for low- and high-MOI analyses.
 -   A suite of plotting functions facilitating visualization of each step in the pipeline.
 -   Expanded support for gRNA assignment and quality control.
--   Interoperability with output from 10X Cell Ranger (available now) and Parse Biosciences (coming soon).
+-   Interoperability with output from 10X Cell Ranger and Parse Biosciences CRISPR Detect.
 -   An [e-book](https://timothy-barry.github.io/sceptre-book/) guiding users through the entire process of analyzing their data using `sceptre`.
 
-`sceptre` v0.9.0 facilitates an entire analysis pipeline for single-cell CRISPR screens, starting from UMI count data obtained from tools like 10X Cell Ranger.
+`sceptre` v0.9.1 facilitates an entire analysis pipeline for single-cell CRISPR screens, starting from UMI count data obtained from tools like 10X Cell Ranger.
 
 ```{=html}
 <!--

diff --git a/README.md b/README.md
@@ -18,9 +18,9 @@ statistical rigor, computational efficiency, and ease of use.
 
 <!-- badges: end -->
 
-## Release of `sceptre` v0.9.0
+## Release of `sceptre` v0.9.1
 
-We are excited to announce the release of `sceptre` v0.9.0, a
+We are excited to announce the release of `sceptre` v0.9.1, a
 substantial update to the package. This milestone includes the following
 developments:
 
@@ -31,13 +31,13 @@ developments:
 - A suite of plotting functions facilitating visualization of each step
   in the pipeline.
 - Expanded support for gRNA assignment and quality control.
-- Interoperability with output from 10X Cell Ranger (available now) and
-  Parse Biosciences (coming soon).
+- Interoperability with output from 10X Cell Ranger and Parse
+  Biosciences CRISPR Detect.
 - An [e-book](https://timothy-barry.github.io/sceptre-book/) guiding
   users through the entire process of analyzing their data using
   `sceptre`.
 
-`sceptre` v0.9.0 facilitates an entire analysis pipeline for single-cell
+`sceptre` v0.9.1 facilitates an entire analysis pipeline for single-cell
 CRISPR screens, starting from UMI count data obtained from tools like
 10X Cell Ranger.
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -28,6 +28,7 @@ reference:
   contents:
   - import_data
   - import_data_from_cellranger
+  - import_data_from_parse
   - set_analysis_parameters
   - assign_grnas
   - run_qc

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/install.html b/docs/articles/install.html
diff --git a/docs/articles/sceptre.html b/docs/articles/sceptre.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   install: install.html
   sceptre: sceptre.html
-last_built: 2023-10-23T16:53Z
+last_built: 2023-10-24T18:19Z
 urls:
   reference: https://katsevich-lab.github.io/sceptre/reference
   article: https://katsevich-lab.github.io/sceptre/articles

diff --git a/docs/reference/assign_grnas.html b/docs/reference/assign_grnas.html
diff --git a/docs/reference/construct_cis_pairs.html b/docs/reference/construct_cis_pairs.html
diff --git a/docs/reference/construct_positive_control_pairs.html b/docs/reference/construct_positive_control_pairs.html
diff --git a/docs/reference/construct_trans_pairs.html b/docs/reference/construct_trans_pairs.html
diff --git a/docs/reference/gene_position_data_frame_grch38.html b/docs/reference/gene_position_data_frame_grch38.html
diff --git a/docs/reference/get_result.html b/docs/reference/get_result.html
diff --git a/docs/reference/grna_target_data_frame_highmoi.html b/docs/reference/grna_target_data_frame_highmoi.html
diff --git a/docs/reference/highmoi_example_data.html b/docs/reference/highmoi_example_data.html
diff --git a/docs/reference/import_data.html b/docs/reference/import_data.html