From 928f6be47af9d14bec2b43e23171898e6f5795cc Mon Sep 17 00:00:00 2001 From: YunningYuan <152803394+YunningYuan@users.noreply.github.com> Date: Sat, 18 Jan 2025 08:21:34 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20neurogen?= =?UTF-8?q?omics/Power=5FAnalysis=5Fpackage@473713ea62dba5137897f9249d265c?= =?UTF-8?q?37fdcf10a4=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/getting_started.html | 6 ++---- articles/poweranalysis.html | 6 ++---- authors.html | 2 +- index.html | 2 +- pkgdown.yml | 4 ++-- reference/DGE_analysis.html | 2 +- reference/compute_downsampled_corr.html | 2 +- reference/correlation_analysis.html | 2 +- reference/correlation_boxplots.html | 2 +- reference/differential_expression.html | 2 +- reference/downsampling_DEanalysis.html | 2 +- reference/downsampling_corrplots.html | 2 +- reference/downsampling_range.html | 2 +- reference/make_pseudobulk.html | 2 +- reference/plot_celltype_correlation.html | 2 +- reference/plot_de_analysis.html | 2 +- reference/plot_mean_correlation.html | 2 +- reference/power_analysis.html | 2 +- reference/power_plots.html | 2 +- reference/preliminary_plots.html | 2 +- reference/random_permutations.html | 2 +- reference/sample_cells.html | 2 +- reference/sample_individuals.html | 2 +- reference/sex_chromosome_DEGs.html | 2 +- reference/subset_pairs.html | 2 +- reference/validate_input_parameters_correlation.html | 2 +- reference/validate_input_parameters_de.html | 2 +- reference/validate_input_parameters_power.html | 2 +- reference/within_data_correlation.html | 2 +- 29 files changed, 32 insertions(+), 36 deletions(-) diff --git a/articles/getting_started.html b/articles/getting_started.html index 65c16a3..d8e1572 100644 --- a/articles/getting_started.html +++ b/articles/getting_started.html @@ -80,7 +80,7 @@

Getting Started

- Source: vignettes/getting_started.Rmd + Source: vignettes/getting_started.Rmd @@ -115,9 +115,7 @@

IntroductionSetup 

-library(poweranalysis)
-#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
-#>   object 'type_sum.accel' not found
+library(poweranalysis) diff --git a/articles/poweranalysis.html b/articles/poweranalysis.html index 713848b..9f5c7e1 100644 --- a/articles/poweranalysis.html +++ b/articles/poweranalysis.html @@ -80,7 +80,7 @@

Power Analysis

- Source: vignettes/poweranalysis.Rmd + Source: vignettes/poweranalysis.Rmd @@ -130,9 +130,7 @@

InstallationSetup 

-library(poweranalysis)
-#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
-#>   object 'type_sum.accel' not found
+library(poweranalysis)


diff --git a/authors.html b/authors.html index 5694222..f1468f9 100644 --- a/authors.html +++ b/authors.html @@ -74,7 +74,7 @@

Authors and Citation

Citation

- Source: DESCRIPTION + Source: DESCRIPTION
diff --git a/index.html b/index.html index c4432ea..f943501 100644 --- a/index.html +++ b/index.html @@ -82,7 +82,7 @@ Power Analysis
Power Analysis for Differential Expression in scRNA-seq data


R build status
License: MIT + file LICENSE

-

Authors: Salman Fawad, Alan Murphy, Nathan Skene
Updated: Jan-04-2025

+

Authors: Salman Fawad, Alan Murphy, Nathan Skene
Updated: Jan-18-2025

Introduction

diff --git a/pkgdown.yml b/pkgdown.yml index 5570098..b8fbeae 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,7 +1,7 @@ -pandoc: 3.6.1 +pandoc: 3.6.2 pkgdown: 2.1.1 pkgdown_sha: ~ articles: getting_started: getting_started.html poweranalysis: poweranalysis.html -last_built: 2025-01-04T04:02Z +last_built: 2025-01-18T08:20Z diff --git a/reference/DGE_analysis.html b/reference/DGE_analysis.html index 99433d8..43b24ab 100644 --- a/reference/DGE_analysis.html +++ b/reference/DGE_analysis.html @@ -54,7 +54,7 @@

Perform differential expression analysis across cell types based on single cell data with Pseudobulk approach. Returns the results of this differential expression analysis

- Source: R/DGE_analysis.R + Source: R/DGE_analysis.R
diff --git a/reference/compute_downsampled_corr.html b/reference/compute_downsampled_corr.html index a0738b2..3312e8a 100644 --- a/reference/compute_downsampled_corr.html +++ b/reference/compute_downsampled_corr.html @@ -54,7 +54,7 @@

For a given down-sampled DE output, computes the correlation of the log-foldchange of the DEGs (at specified p-value) for a given dataset (celltype)

- Source: R/compute_downsampled_corr.r + Source: R/compute_downsampled_corr.r
diff --git a/reference/correlation_analysis.html b/reference/correlation_analysis.html index 4664970..58dba09 100644 --- a/reference/correlation_analysis.html +++ b/reference/correlation_analysis.html @@ -54,7 +54,7 @@

Runs correlation analysis pipeline

- Source: R/correlation_analysis.r + Source: R/correlation_analysis.r
diff --git a/reference/correlation_boxplots.html b/reference/correlation_boxplots.html index 57f56d5..f5058ab 100644 --- a/reference/correlation_boxplots.html +++ b/reference/correlation_boxplots.html @@ -54,7 +54,7 @@

Obtain box plots for the correlations of all celltypes, and the mean correlations at a specified cutoff p-value

- Source: R/correlation_boxplots.r + Source: R/correlation_boxplots.r
diff --git a/reference/differential_expression.html b/reference/differential_expression.html index cfc80da..5fec475 100644 --- a/reference/differential_expression.html +++ b/reference/differential_expression.html @@ -54,7 +54,7 @@

Differential Expression Analysis using edgeR LRT on pseudobulk data

- Source: R/differential_expression.R + Source: R/differential_expression.R
diff --git a/reference/downsampling_DEanalysis.html b/reference/downsampling_DEanalysis.html index 14c1ebc..b1a4a5c 100644 --- a/reference/downsampling_DEanalysis.html +++ b/reference/downsampling_DEanalysis.html @@ -54,7 +54,7 @@

Downsample the dataset, based either on the individuals or cells, and run DE analysis on each downsampled output. Save results in a dataframe

- Source: R/downsampling_DEanalysis.r + Source: R/downsampling_DEanalysis.r
diff --git a/reference/downsampling_corrplots.html b/reference/downsampling_corrplots.html index 884dfb5..ec2971e 100644 --- a/reference/downsampling_corrplots.html +++ b/reference/downsampling_corrplots.html @@ -54,7 +54,7 @@

Create correlation plots of the effect sizes of the top 1000 and top 500 DEGs

- Source: R/downsampling_corrplots.r + Source: R/downsampling_corrplots.r
diff --git a/reference/downsampling_range.html b/reference/downsampling_range.html index 6f4bb60..5378057 100644 --- a/reference/downsampling_range.html +++ b/reference/downsampling_range.html @@ -54,7 +54,7 @@

Obtain the range of values to downsample at (either for individuals, or mean number of cells per individual)

- Source: R/downsampling_range.r + Source: R/downsampling_range.r
diff --git a/reference/make_pseudobulk.html b/reference/make_pseudobulk.html index 267ed84..db0d279 100644 --- a/reference/make_pseudobulk.html +++ b/reference/make_pseudobulk.html @@ -54,7 +54,7 @@

Calculate the summed pseudobulk values for an SCE object based on one single cell type only. Ensure to filter SCE to pass one cell type's data.

- Source: R/make_pseudobulk.R + Source: R/make_pseudobulk.R
diff --git a/reference/plot_celltype_correlation.html b/reference/plot_celltype_correlation.html index 38fbd6d..5712aad 100644 --- a/reference/plot_celltype_correlation.html +++ b/reference/plot_celltype_correlation.html @@ -54,7 +54,7 @@

Computes the correlation of the log-foldchange of the DEGs (at specified p-value) for a given celltype, across all datasets

- Source: R/plot_celltype_correlation.r + Source: R/plot_celltype_correlation.r
diff --git a/reference/plot_de_analysis.html b/reference/plot_de_analysis.html index e657379..fe2d9e2 100644 --- a/reference/plot_de_analysis.html +++ b/reference/plot_de_analysis.html @@ -54,7 +54,7 @@

Create differential expression analysis plots. Run by DGE_analysis()

- Source: R/plot_de_analysis.R + Source: R/plot_de_analysis.R
diff --git a/reference/plot_mean_correlation.html b/reference/plot_mean_correlation.html index de686cc..0b0034c 100644 --- a/reference/plot_mean_correlation.html +++ b/reference/plot_mean_correlation.html @@ -54,7 +54,7 @@

Obtain the average correlation (across celltypes) at a specified cutoff p-value

- Source: R/plot_mean_correlation.r + Source: R/plot_mean_correlation.r
diff --git a/reference/power_analysis.html b/reference/power_analysis.html index 4ca6447..eae1d25 100644 --- a/reference/power_analysis.html +++ b/reference/power_analysis.html @@ -54,7 +54,7 @@

Runs entire power analysis pipeline

- Source: R/power_analysis.r + Source: R/power_analysis.r
diff --git a/reference/power_plots.html b/reference/power_plots.html index 8237764..e8ffa44 100644 --- a/reference/power_plots.html +++ b/reference/power_plots.html @@ -54,7 +54,7 @@

Create plots for power analysis, with down-sampling based either on the individuals or cells

- Source: R/power_plots.r + Source: R/power_plots.r
diff --git a/reference/preliminary_plots.html b/reference/preliminary_plots.html index 8311b2b..0c69500 100644 --- a/reference/preliminary_plots.html +++ b/reference/preliminary_plots.html @@ -54,7 +54,7 @@

Create preliminary plots for data exploration

- Source: R/preliminary_plots.r + Source: R/preliminary_plots.r
diff --git a/reference/random_permutations.html b/reference/random_permutations.html index a2234c7..af9d861 100644 --- a/reference/random_permutations.html +++ b/reference/random_permutations.html @@ -54,7 +54,7 @@

Obtain highly randomised permutations of a specified dataset (based on sex labels), while maintaining consistency with the sample ID

- Source: R/random_permutations.r + Source: R/random_permutations.r
diff --git a/reference/sample_cells.html b/reference/sample_cells.html index 3ade819..e35bf3b 100644 --- a/reference/sample_cells.html +++ b/reference/sample_cells.html @@ -54,7 +54,7 @@

Sample the data for a specified mean number of cells (per sample) from the dataset

- Source: R/sample_cells.r + Source: R/sample_cells.r
diff --git a/reference/sample_individuals.html b/reference/sample_individuals.html index 77d3606..723e31b 100644 --- a/reference/sample_individuals.html +++ b/reference/sample_individuals.html @@ -54,7 +54,7 @@

Sample the data for a specified number of individuals from the dataset

- Source: R/sample_individuals.r + Source: R/sample_individuals.r
diff --git a/reference/sex_chromosome_DEGs.html b/reference/sex_chromosome_DEGs.html index 4d692bc..db9eae0 100644 --- a/reference/sex_chromosome_DEGs.html +++ b/reference/sex_chromosome_DEGs.html @@ -54,7 +54,7 @@

Given a DGE analysis output, this outputs a subset of the analysis with the genes laying only on the sex chromosomes (X/Y)

- Source: R/sex_chromosome_DEGs.r + Source: R/sex_chromosome_DEGs.r
diff --git a/reference/subset_pairs.html b/reference/subset_pairs.html index 30dd761..2c5a636 100644 --- a/reference/subset_pairs.html +++ b/reference/subset_pairs.html @@ -54,7 +54,7 @@

Obtain independent pairs of subsets of a specified dataset, based on sample ID

- Source: R/subset_pairs.r + Source: R/subset_pairs.r
diff --git a/reference/validate_input_parameters_correlation.html b/reference/validate_input_parameters_correlation.html index 4dc2d85..b2bcf8e 100644 --- a/reference/validate_input_parameters_correlation.html +++ b/reference/validate_input_parameters_correlation.html @@ -54,7 +54,7 @@

Tests input parameters for functions

- Source: R/validate_input_parameters_correlation.r + Source: R/validate_input_parameters_correlation.r
diff --git a/reference/validate_input_parameters_de.html b/reference/validate_input_parameters_de.html index a5033c3..11af7b5 100644 --- a/reference/validate_input_parameters_de.html +++ b/reference/validate_input_parameters_de.html @@ -54,7 +54,7 @@

Validate that there are no user input errors for the differential expression analysis - sc.cell.type.de

- Source: R/validate_input_parameters_de.R + Source: R/validate_input_parameters_de.R
diff --git a/reference/validate_input_parameters_power.html b/reference/validate_input_parameters_power.html index dcd9c05..5abc420 100644 --- a/reference/validate_input_parameters_power.html +++ b/reference/validate_input_parameters_power.html @@ -54,7 +54,7 @@

Tests input parameters for functions

- Source: R/validate_input_parameters_power.r + Source: R/validate_input_parameters_power.r
diff --git a/reference/within_data_correlation.html b/reference/within_data_correlation.html index f99ef76..71fcf3b 100644 --- a/reference/within_data_correlation.html +++ b/reference/within_data_correlation.html @@ -54,7 +54,7 @@

Create correlation plots of the effect sizes, between random permutations and subsets of a given dataset

- Source: R/within_data_correlation.r + Source: R/within_data_correlation.r