From f7793172e38ec14dcf12898419c00b1b35043840 Mon Sep 17 00:00:00 2001 From: jleechung Date: Thu, 9 May 2024 14:29:44 +0100 Subject: [PATCH] Update docs --- README.Rmd | 1 + README.md | 8 +- docs/404.html | 2 +- docs/LICENSE-text.html | 24 ++-- docs/articles/batch-correction.html | 148 ++++++++++++------------ docs/articles/domain-segment.html | 6 +- docs/articles/index.html | 2 +- docs/articles/multi-sample.html | 149 ++++++++++++------------- docs/articles/parameter-selection.html | 8 +- docs/authors.html | 2 +- docs/index.html | 11 +- docs/news/index.html | 2 +- docs/pkgdown.yml | 4 +- docs/reference/Banksy-package.html | 2 +- docs/reference/clusterBanksy.html | 2 +- docs/reference/clusterNames.html | 2 +- docs/reference/compareClusters.html | 2 +- docs/reference/computeBanksy.html | 2 +- docs/reference/connectClusters.html | 2 +- docs/reference/getBanksyMatrix.html | 2 +- docs/reference/hippocampus.html | 2 +- docs/reference/index.html | 2 +- docs/reference/rings.html | 2 +- docs/reference/runBanksyPCA.html | 2 +- docs/reference/runBanksyUMAP.html | 2 +- docs/reference/simulateDataset.html | 2 +- docs/reference/smoothLabels.html | 2 +- 27 files changed, 199 insertions(+), 196 deletions(-) diff --git a/README.Rmd b/README.Rmd index cde8cb5..47a80df 100644 --- a/README.Rmd +++ b/README.Rmd @@ -38,6 +38,7 @@ details, check out: - a [tweetorial](https://x.com/shyam_lab/status/1762648072360792479?s=20) on BANKSY, - a set of [vignettes](https://prabhakarlab.github.io/Banksy) showing basic usage, +- usage compatibility with Seurat ([here](https://github.com/satijalab/seurat-wrappers/blob/master/docs/banksy.md) and [here](https://satijalab.org/seurat/articles/visiumhd_analysis_vignette#identifying-spatially-defined-tissue-domains)), - a [Python version](https://github.com/prabhakarlab/Banksy_py) of this package, - a [Zenodo archive](https://zenodo.org/records/10258795) containing scripts to reproduce the analyses in the paper, and the corresponding diff --git a/README.md b/README.md index 57784ee..fd63947 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,10 @@ datasets. For more details, check out: on BANKSY, - a set of [vignettes](https://prabhakarlab.github.io/Banksy) showing basic usage, +- usage compatibility with Seurat + ([here](https://github.com/satijalab/seurat-wrappers/blob/master/docs/banksy.md) + and + [here](https://satijalab.org/seurat/articles/visiumhd_analysis_vignette#identifying-spatially-defined-tissue-domains)), - a [Python version](https://github.com/prabhakarlab/Banksy_py) of this package, - a [Zenodo archive](https://zenodo.org/records/10258795) containing @@ -221,7 +225,7 @@ plot_grid( Runtime for analysis - #> Time difference of 55.9195 secs + #> Time difference of 57.44879 secs
@@ -257,7 +261,7 @@ sessionInfo() #> [9] GenomicRanges_1.54.1 GenomeInfoDb_1.38.6 #> [11] IRanges_2.36.0 S4Vectors_0.40.2 #> [13] BiocGenerics_0.48.1 MatrixGenerics_1.14.0 -#> [15] matrixStats_1.2.0 Banksy_0.99.9 +#> [15] matrixStats_1.2.0 Banksy_0.99.12 #> #> loaded via a namespace (and not attached): #> [1] tidyselect_1.2.0 viridisLite_0.4.2 diff --git a/docs/404.html b/docs/404.html index 5abffa5..97cc98c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 6c3a514..88f8a91 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 @@ -68,11 +68,15 @@

License

 USER LICENSE for the software suite BANKSY
 
+TLDR (see below for details). 
+Academic usage: MIT License
+Commercial Usage: Restrictions applicable, see below. 
+
 Authorship and Copyright (c) 
 2022; Vipul Singhal, Joseph Lee
 
 References of associated scientific publications
-1) Vipul Singhal, Nigel Chou, Joseph Lee, Jinyue Liu, Wan Kee Chock, Li Lin, Yun-Ching Chang, Erica Teo, Hwee Kuan Lee, Kok Hao Chen, Shyam Prabhakar. BANKSY: A Spatial Omics Algorithm that Unifies Cell Type Clustering and Tissue Domain Segmentation. bioRxiv. doi: 10.1101/2022.04.14.488259 (2022).
+1) Singhal, V., Chou, N., Lee, J. et al. BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis. Nat Genet 56, 431–441 (2024). https://doi.org/10.1038/s41588-024-01664-3
 
 ***
 
@@ -106,11 +110,13 @@ 
License

 
 The copyright messages (if any) will not be modified or suppressed. The software package will always remain associated with this license agreement.
 
-3. Academic (non-commercial) usage
+3. Academic (non-commercial) usage: MIT License
+
+Copyright (c) <2022> <Vipul Singhal, Joseph Lee>
 
-Permission is hereby granted, free of charge for academic purposes, to obtaining a copy of this software, to use, copy, modify it and to integrate it into other software within the same research team and its immediate collaborators, to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission/license notice shall be included in all copies or substantial portions of the Software. 
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 
-The user will not redistribute this software beyond the range allowed in this academic license exception but refer the interested party to the author and/or its distribution site. 
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 
 4. Commercial usage
 
@@ -118,13 +124,7 @@ 
License

 
 Any software package that contains this software or parts of it can only be commercialized with a license agreement issued by the author. 
 
-5. Bugs and other erroneous behaviour of the software
-
-The user will report bugs and errors observed in using the software to the author as soon as possible, without delay. 
-
-The author will provide software user support, maintenance and software updates on a good will basis. 
-
-6. Warranty and liability
+5. Warranty and liability
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
 IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING OUT OF OR IN CONNECTION WITH THE USE, PERFORMANCE OF THIS SOFTWARE OR ANY OTHER DEALINGS WITH IT, WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF LIABILITY. 
diff --git a/docs/articles/batch-correction.html b/docs/articles/batch-correction.html
index 2824bde..c24f25b 100644
--- a/docs/articles/batch-correction.html
+++ b/docs/articles/batch-correction.html
@@ -33,7 +33,7 @@
       
       
         Banksy
-        0.99.9
+        0.99.12
       
     
 
@@ -116,7 +116,6 @@ 
Spatial data integration with Harmony (10x
 library(scater)
 library(cowplot)
 library(ggplot2)
-library(ggspavis)
 
 SEED <- 1000
@@ -280,7 +279,7 @@

Run Harmony on BANKSY’s embeddingSession information

Vignette runtime:

-
#> Time difference of 2.265773 mins
+
#> Time difference of 2.360226 mins
 sessionInfo()
 #> R version 4.3.2 (2023-10-31)
@@ -292,7 +291,7 @@ 
Session information#> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
 #> 
 #> locale:
-#> [1] C/en_US.UTF-8/C/C/C/C
+#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
 #> 
 #> time zone: Europe/London
 #> tzcode source: internal
@@ -304,19 +303,19 @@ 
Session information#> other attached packages:
 #>  [1] ExperimentHub_2.10.0        AnnotationHub_3.10.0       
 #>  [3] BiocFileCache_2.10.1        dbplyr_2.4.0               
-#>  [5] spatialLIBD_1.14.1          ggspavis_1.8.0             
-#>  [7] cowplot_1.1.3               scater_1.30.1              
-#>  [9] ggplot2_3.4.4               harmony_1.2.0              
-#> [11] Rcpp_1.0.12                 data.table_1.15.0          
-#> [13] scran_1.30.2                scuttle_1.12.0             
-#> [15] Seurat_5.0.1                SeuratObject_5.0.1         
-#> [17] sp_2.1-3                    SpatialExperiment_1.12.0   
-#> [19] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
-#> [21] Biobase_2.62.0              GenomicRanges_1.54.1       
-#> [23] GenomeInfoDb_1.38.6         IRanges_2.36.0             
-#> [25] S4Vectors_0.40.2            BiocGenerics_0.48.1        
-#> [27] MatrixGenerics_1.14.0       matrixStats_1.2.0          
-#> [29] Banksy_0.99.9               BiocStyle_2.30.0           
+#>  [5] spatialLIBD_1.14.1          cowplot_1.1.3              
+#>  [7] scater_1.30.1               ggplot2_3.4.4              
+#>  [9] harmony_1.2.0               Rcpp_1.0.12                
+#> [11] data.table_1.15.0           scran_1.30.2               
+#> [13] scuttle_1.12.0              Seurat_5.0.1               
+#> [15] SeuratObject_5.0.1          sp_2.1-3                   
+#> [17] SpatialExperiment_1.12.0    SingleCellExperiment_1.24.0
+#> [19] SummarizedExperiment_1.32.0 Biobase_2.62.0             
+#> [21] GenomicRanges_1.54.1        GenomeInfoDb_1.38.6        
+#> [23] IRanges_2.36.0              S4Vectors_0.40.2           
+#> [25] BiocGenerics_0.48.1         MatrixGenerics_1.14.0      
+#> [27] matrixStats_1.2.0           Banksy_0.99.12             
+#> [29] BiocStyle_2.30.0           
 #> 
 #> loaded via a namespace (and not attached):
 #>   [1] fs_1.6.3                      spatstat.sparse_3.0-3        
@@ -360,64 +359,63 @@ 
Session information#>  [77] gtable_0.3.4                  rematch2_2.1.2               
 #>  [79] cachem_1.0.8                  xfun_0.42                    
 #>  [81] S4Arrays_1.2.0                mime_0.12                    
-#>  [83] ggside_0.2.3                  survival_3.5-7               
-#>  [85] RcppHungarian_0.3             iterators_1.0.14             
-#>  [87] fields_15.2                   statmod_1.5.0                
-#>  [89] bluster_1.12.0                interactiveDisplayBase_1.40.0
-#>  [91] ellipsis_0.3.2                fitdistrplus_1.1-11          
-#>  [93] ROCR_1.0-11                   nlme_3.1-164                 
-#>  [95] bit64_4.0.5                   filelock_1.0.3               
-#>  [97] RcppAnnoy_0.0.22              bslib_0.6.1                  
-#>  [99] irlba_2.3.5.1                 vipor_0.4.7                  
-#> [101] KernSmooth_2.23-22            colorspace_2.1-0             
-#> [103] DBI_1.2.1                     tidyselect_1.2.0             
-#> [105] curl_5.2.0                    bit_4.0.5                    
-#> [107] compiler_4.3.2                BiocNeighbors_1.20.2         
-#> [109] desc_1.4.3                    DelayedArray_0.28.0          
-#> [111] plotly_4.10.4                 rtracklayer_1.62.0           
-#> [113] bookdown_0.37                 scales_1.3.0                 
-#> [115] lmtest_0.9-40                 rappdirs_0.3.3               
-#> [117] stringr_1.5.1                 digest_0.6.34                
-#> [119] goftest_1.2-3                 spatstat.utils_3.0-4         
-#> [121] rmarkdown_2.25                benchmarkmeData_1.0.4        
-#> [123] RhpcBLASctl_0.23-42           XVector_0.42.0               
-#> [125] htmltools_0.5.7               pkgconfig_2.0.3              
-#> [127] sparseMatrixStats_1.14.0      highr_0.10                   
-#> [129] fastmap_1.1.1                 rlang_1.1.3                  
-#> [131] htmlwidgets_1.6.4             shiny_1.8.0                  
-#> [133] DelayedMatrixStats_1.24.0     farver_2.1.1                 
-#> [135] jquerylib_0.1.4               zoo_1.8-12                   
-#> [137] jsonlite_1.8.8                BiocParallel_1.36.0          
-#> [139] mclust_6.0.1                  config_0.3.2                 
-#> [141] BiocSingular_1.18.0           RCurl_1.98-1.14              
-#> [143] magrittr_2.0.3                GenomeInfoDbData_1.2.11      
-#> [145] dotCall64_1.1-1               patchwork_1.2.0              
-#> [147] munsell_0.5.0                 viridis_0.6.5                
-#> [149] reticulate_1.35.0             leidenAlg_1.1.2              
-#> [151] stringi_1.8.3                 zlibbioc_1.48.0              
-#> [153] MASS_7.3-60.0.1               plyr_1.8.9                   
-#> [155] parallel_4.3.2                listenv_0.9.1                
-#> [157] ggrepel_0.9.5                 deldir_2.0-2                 
-#> [159] Biostrings_2.70.2             sccore_1.0.4                 
-#> [161] splines_4.3.2                 tensor_1.5                   
-#> [163] locfit_1.5-9.8                igraph_2.0.1.1               
-#> [165] spatstat.geom_3.2-8           RcppHNSW_0.6.0               
-#> [167] reshape2_1.4.4                ScaledMatrix_1.10.0          
-#> [169] XML_3.99-0.16.1               BiocVersion_3.18.1           
-#> [171] evaluate_0.23                 golem_0.4.1                  
-#> [173] BiocManager_1.30.22           foreach_1.5.2                
-#> [175] httpuv_1.6.14                 RANN_2.6.1                   
-#> [177] tidyr_1.3.1                   purrr_1.0.2                  
-#> [179] polyclip_1.10-6               benchmarkme_1.0.8            
-#> [181] future_1.33.1                 scattermore_1.2              
-#> [183] rsvd_1.0.5                    xtable_1.8-4                 
-#> [185] restfulr_0.0.15               RSpectra_0.16-1              
-#> [187] later_1.3.2                   viridisLite_0.4.2            
-#> [189] ragg_1.2.7                    tibble_3.2.1                 
-#> [191] GenomicAlignments_1.38.2      AnnotationDbi_1.64.1         
-#> [193] memoise_2.0.1                 beeswarm_0.4.0               
-#> [195] cluster_2.1.6                 shinyWidgets_0.8.1           
-#> [197] globals_0.16.2
+#> [83] survival_3.5-7 RcppHungarian_0.3 +#> [85] iterators_1.0.14 fields_15.2 +#> [87] statmod_1.5.0 bluster_1.12.0 +#> [89] interactiveDisplayBase_1.40.0 ellipsis_0.3.2 +#> [91] fitdistrplus_1.1-11 ROCR_1.0-11 +#> [93] nlme_3.1-164 bit64_4.0.5 +#> [95] filelock_1.0.3 RcppAnnoy_0.0.22 +#> [97] bslib_0.6.1 irlba_2.3.5.1 +#> [99] vipor_0.4.7 KernSmooth_2.23-22 +#> [101] colorspace_2.1-0 DBI_1.2.1 +#> [103] tidyselect_1.2.0 bit_4.0.5 +#> [105] compiler_4.3.2 curl_5.2.0 +#> [107] BiocNeighbors_1.20.2 desc_1.4.3 +#> [109] DelayedArray_0.28.0 plotly_4.10.4 +#> [111] rtracklayer_1.62.0 bookdown_0.37 +#> [113] scales_1.3.0 lmtest_0.9-40 +#> [115] rappdirs_0.3.3 stringr_1.5.1 +#> [117] digest_0.6.34 goftest_1.2-3 +#> [119] spatstat.utils_3.0-4 rmarkdown_2.25 +#> [121] benchmarkmeData_1.0.4 RhpcBLASctl_0.23-42 +#> [123] XVector_0.42.0 htmltools_0.5.7 +#> [125] pkgconfig_2.0.3 sparseMatrixStats_1.14.0 +#> [127] highr_0.10 fastmap_1.1.1 +#> [129] rlang_1.1.3 htmlwidgets_1.6.4 +#> [131] shiny_1.8.0 DelayedMatrixStats_1.24.0 +#> [133] farver_2.1.1 jquerylib_0.1.4 +#> [135] zoo_1.8-12 jsonlite_1.8.8 +#> [137] BiocParallel_1.36.0 mclust_6.0.1 +#> [139] config_0.3.2 BiocSingular_1.18.0 +#> [141] RCurl_1.98-1.14 magrittr_2.0.3 +#> [143] GenomeInfoDbData_1.2.11 dotCall64_1.1-1 +#> [145] patchwork_1.2.0 munsell_0.5.0 +#> [147] viridis_0.6.5 reticulate_1.35.0 +#> [149] leidenAlg_1.1.2 stringi_1.8.3 +#> [151] zlibbioc_1.48.0 MASS_7.3-60.0.1 +#> [153] plyr_1.8.9 parallel_4.3.2 +#> [155] listenv_0.9.1 ggrepel_0.9.5 +#> [157] deldir_2.0-2 Biostrings_2.70.2 +#> [159] sccore_1.0.4 splines_4.3.2 +#> [161] tensor_1.5 locfit_1.5-9.8 +#> [163] igraph_2.0.1.1 spatstat.geom_3.2-8 +#> [165] RcppHNSW_0.6.0 reshape2_1.4.4 +#> [167] ScaledMatrix_1.10.0 XML_3.99-0.16.1 +#> [169] BiocVersion_3.18.1 evaluate_0.23 +#> [171] golem_0.4.1 BiocManager_1.30.22 +#> [173] foreach_1.5.2 httpuv_1.6.14 +#> [175] RANN_2.6.1 tidyr_1.3.1 +#> [177] purrr_1.0.2 polyclip_1.10-6 +#> [179] benchmarkme_1.0.8 future_1.33.1 +#> [181] scattermore_1.2 rsvd_1.0.5 +#> [183] xtable_1.8-4 restfulr_0.0.15 +#> [185] RSpectra_0.16-1 later_1.3.2 +#> [187] viridisLite_0.4.2 ragg_1.2.7 +#> [189] tibble_3.2.1 GenomicAlignments_1.38.2 +#> [191] AnnotationDbi_1.64.1 memoise_2.0.1 +#> [193] beeswarm_0.4.0 cluster_2.1.6 +#> [195] shinyWidgets_0.8.1 globals_0.16.2
diff --git a/docs/articles/domain-segment.html b/docs/articles/domain-segment.html index 951500a..7c4e8e9 100644 --- a/docs/articles/domain-segment.html +++ b/docs/articles/domain-segment.html @@ -33,7 +33,7 @@ Banksy - 0.99.9 + 0.99.12 @@ -209,7 +209,7 @@

Session information#> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 #> #> locale: -#> [1] C/en_US.UTF-8/C/C/C/C +#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 #> #> time zone: Europe/London #> tzcode source: internal @@ -227,7 +227,7 @@

Session information#> [11] IRanges_2.36.0 S4Vectors_0.40.2 #> [13] BiocGenerics_0.48.1 MatrixGenerics_1.14.0 #> [15] matrixStats_1.2.0 data.table_1.15.0 -#> [17] Banksy_0.99.9 BiocStyle_2.30.0 +#> [17] Banksy_0.99.12 BiocStyle_2.30.0 #> #> loaded via a namespace (and not attached): #> [1] bitops_1.0-7 gridExtra_2.3 diff --git a/docs/articles/index.html b/docs/articles/index.html index 24740c5..2b861b8 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/articles/multi-sample.html b/docs/articles/multi-sample.html index e3a2aa1..3d504fd 100644 --- a/docs/articles/multi-sample.html +++ b/docs/articles/multi-sample.html @@ -33,7 +33,7 @@ Banksy - 0.99.9 + 0.99.12 @@ -111,8 +111,7 @@

Multi-sample analysis (10x Visium Human library(scater) library(cowplot) -library(ggplot2) -library(ggspavis) +library(ggplot2)

Loading the data

@@ -366,7 +365,7 @@

Parsing BANKSY outputSession information

Vignette runtime:

-
#> Time difference of 2.566006 mins
+
#> Time difference of 2.687769 mins
 sessionInfo()
 #> R version 4.3.2 (2023-10-31)
@@ -378,7 +377,7 @@ 
Session information#> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
 #> 
 #> locale:
-#> [1] C/en_US.UTF-8/C/C/C/C
+#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
 #> 
 #> time zone: Europe/London
 #> tzcode source: internal
@@ -390,25 +389,25 @@ 
Session information#> other attached packages:
 #>  [1] ExperimentHub_2.10.0        AnnotationHub_3.10.0       
 #>  [3] BiocFileCache_2.10.1        dbplyr_2.4.0               
-#>  [5] spatialLIBD_1.14.1          ggspavis_1.8.0             
-#>  [7] cowplot_1.1.3               scater_1.30.1              
-#>  [9] ggplot2_3.4.4               scuttle_1.12.0             
-#> [11] Seurat_5.0.1                SeuratObject_5.0.1         
-#> [13] sp_2.1-3                    SpatialExperiment_1.12.0   
-#> [15] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
-#> [17] Biobase_2.62.0              GenomicRanges_1.54.1       
-#> [19] GenomeInfoDb_1.38.6         IRanges_2.36.0             
-#> [21] S4Vectors_0.40.2            BiocGenerics_0.48.1        
-#> [23] MatrixGenerics_1.14.0       matrixStats_1.2.0          
-#> [25] Banksy_0.99.9               BiocStyle_2.30.0           
+#>  [5] spatialLIBD_1.14.1          cowplot_1.1.3              
+#>  [7] scater_1.30.1               ggplot2_3.4.4              
+#>  [9] scuttle_1.12.0              Seurat_5.0.1               
+#> [11] SeuratObject_5.0.1          sp_2.1-3                   
+#> [13] SpatialExperiment_1.12.0    SingleCellExperiment_1.24.0
+#> [15] SummarizedExperiment_1.32.0 Biobase_2.62.0             
+#> [17] GenomicRanges_1.54.1        GenomeInfoDb_1.38.6        
+#> [19] IRanges_2.36.0              S4Vectors_0.40.2           
+#> [21] BiocGenerics_0.48.1         MatrixGenerics_1.14.0      
+#> [23] matrixStats_1.2.0           Banksy_0.99.12             
+#> [25] BiocStyle_2.30.0           
 #> 
 #> loaded via a namespace (and not attached):
 #>   [1] fs_1.6.3                      spatstat.sparse_3.0-3        
 #>   [3] bitops_1.0-7                  doParallel_1.0.17            
 #>   [5] httr_1.4.7                    RColorBrewer_1.1-3           
 #>   [7] tools_4.3.2                   sctransform_0.4.1            
-#>   [9] DT_0.31                       utf8_1.2.4                   
-#>  [11] R6_2.5.1                      lazyeval_0.2.2               
+#>   [9] utf8_1.2.4                    R6_2.5.1                     
+#>  [11] DT_0.31                       lazyeval_0.2.2               
 #>  [13] uwot_0.1.16                   withr_3.0.0                  
 #>  [15] gridExtra_2.3                 progressr_0.14.0             
 #>  [17] cli_3.6.2                     textshaping_0.3.7            
@@ -442,63 +441,63 @@ 
Session information#>  [73] gtable_0.3.4                  rematch2_2.1.2               
 #>  [75] cachem_1.0.8                  xfun_0.42                    
 #>  [77] S4Arrays_1.2.0                mime_0.12                    
-#>  [79] ggside_0.2.3                  survival_3.5-7               
-#>  [81] RcppHungarian_0.3             iterators_1.0.14             
-#>  [83] fields_15.2                   statmod_1.5.0                
-#>  [85] interactiveDisplayBase_1.40.0 ellipsis_0.3.2               
-#>  [87] fitdistrplus_1.1-11           ROCR_1.0-11                  
-#>  [89] nlme_3.1-164                  bit64_4.0.5                  
-#>  [91] filelock_1.0.3                RcppAnnoy_0.0.22             
-#>  [93] bslib_0.6.1                   irlba_2.3.5.1                
-#>  [95] vipor_0.4.7                   KernSmooth_2.23-22           
-#>  [97] colorspace_2.1-0              DBI_1.2.1                    
-#>  [99] tidyselect_1.2.0              bit_4.0.5                    
-#> [101] compiler_4.3.2                curl_5.2.0                   
-#> [103] BiocNeighbors_1.20.2          desc_1.4.3                   
-#> [105] DelayedArray_0.28.0           plotly_4.10.4                
-#> [107] rtracklayer_1.62.0            bookdown_0.37                
-#> [109] scales_1.3.0                  lmtest_0.9-40                
-#> [111] rappdirs_0.3.3                stringr_1.5.1                
-#> [113] digest_0.6.34                 goftest_1.2-3                
-#> [115] spatstat.utils_3.0-4          rmarkdown_2.25               
-#> [117] benchmarkmeData_1.0.4         XVector_0.42.0               
-#> [119] htmltools_0.5.7               pkgconfig_2.0.3              
-#> [121] sparseMatrixStats_1.14.0      highr_0.10                   
-#> [123] fastmap_1.1.1                 rlang_1.1.3                  
-#> [125] htmlwidgets_1.6.4             shiny_1.8.0                  
-#> [127] DelayedMatrixStats_1.24.0     farver_2.1.1                 
-#> [129] jquerylib_0.1.4               zoo_1.8-12                   
-#> [131] jsonlite_1.8.8                BiocParallel_1.36.0          
-#> [133] mclust_6.0.1                  config_0.3.2                 
-#> [135] BiocSingular_1.18.0           RCurl_1.98-1.14              
-#> [137] magrittr_2.0.3                GenomeInfoDbData_1.2.11      
-#> [139] dotCall64_1.1-1               patchwork_1.2.0              
-#> [141] munsell_0.5.0                 Rcpp_1.0.12                  
-#> [143] viridis_0.6.5                 reticulate_1.35.0            
-#> [145] leidenAlg_1.1.2               stringi_1.8.3                
-#> [147] zlibbioc_1.48.0               MASS_7.3-60.0.1              
-#> [149] plyr_1.8.9                    parallel_4.3.2               
-#> [151] listenv_0.9.1                 ggrepel_0.9.5                
-#> [153] deldir_2.0-2                  Biostrings_2.70.2            
-#> [155] sccore_1.0.4                  splines_4.3.2                
-#> [157] tensor_1.5                    locfit_1.5-9.8               
-#> [159] igraph_2.0.1.1                spatstat.geom_3.2-8          
-#> [161] RcppHNSW_0.6.0                reshape2_1.4.4               
-#> [163] ScaledMatrix_1.10.0           XML_3.99-0.16.1              
-#> [165] BiocVersion_3.18.1            evaluate_0.23                
-#> [167] golem_0.4.1                   BiocManager_1.30.22          
-#> [169] foreach_1.5.2                 httpuv_1.6.14                
-#> [171] RANN_2.6.1                    tidyr_1.3.1                  
-#> [173] purrr_1.0.2                   polyclip_1.10-6              
-#> [175] benchmarkme_1.0.8             future_1.33.1                
-#> [177] scattermore_1.2               rsvd_1.0.5                   
-#> [179] xtable_1.8-4                  restfulr_0.0.15              
-#> [181] RSpectra_0.16-1               later_1.3.2                  
-#> [183] viridisLite_0.4.2             ragg_1.2.7                   
-#> [185] tibble_3.2.1                  GenomicAlignments_1.38.2     
-#> [187] memoise_2.0.1                 beeswarm_0.4.0               
-#> [189] AnnotationDbi_1.64.1          cluster_2.1.6                
-#> [191] shinyWidgets_0.8.1            globals_0.16.2
+#> [79] survival_3.5-7 RcppHungarian_0.3 +#> [81] iterators_1.0.14 fields_15.2 +#> [83] statmod_1.5.0 interactiveDisplayBase_1.40.0 +#> [85] ellipsis_0.3.2 fitdistrplus_1.1-11 +#> [87] ROCR_1.0-11 nlme_3.1-164 +#> [89] bit64_4.0.5 filelock_1.0.3 +#> [91] RcppAnnoy_0.0.22 bslib_0.6.1 +#> [93] irlba_2.3.5.1 vipor_0.4.7 +#> [95] KernSmooth_2.23-22 colorspace_2.1-0 +#> [97] DBI_1.2.1 tidyselect_1.2.0 +#> [99] bit_4.0.5 compiler_4.3.2 +#> [101] curl_5.2.0 BiocNeighbors_1.20.2 +#> [103] desc_1.4.3 DelayedArray_0.28.0 +#> [105] plotly_4.10.4 rtracklayer_1.62.0 +#> [107] bookdown_0.37 scales_1.3.0 +#> [109] lmtest_0.9-40 rappdirs_0.3.3 +#> [111] stringr_1.5.1 digest_0.6.34 +#> [113] goftest_1.2-3 spatstat.utils_3.0-4 +#> [115] rmarkdown_2.25 benchmarkmeData_1.0.4 +#> [117] XVector_0.42.0 htmltools_0.5.7 +#> [119] pkgconfig_2.0.3 sparseMatrixStats_1.14.0 +#> [121] highr_0.10 fastmap_1.1.1 +#> [123] rlang_1.1.3 htmlwidgets_1.6.4 +#> [125] shiny_1.8.0 DelayedMatrixStats_1.24.0 +#> [127] farver_2.1.1 jquerylib_0.1.4 +#> [129] zoo_1.8-12 jsonlite_1.8.8 +#> [131] BiocParallel_1.36.0 mclust_6.0.1 +#> [133] config_0.3.2 BiocSingular_1.18.0 +#> [135] RCurl_1.98-1.14 magrittr_2.0.3 +#> [137] GenomeInfoDbData_1.2.11 dotCall64_1.1-1 +#> [139] patchwork_1.2.0 munsell_0.5.0 +#> [141] Rcpp_1.0.12 viridis_0.6.5 +#> [143] reticulate_1.35.0 leidenAlg_1.1.2 +#> [145] stringi_1.8.3 zlibbioc_1.48.0 +#> [147] MASS_7.3-60.0.1 plyr_1.8.9 +#> [149] parallel_4.3.2 listenv_0.9.1 +#> [151] ggrepel_0.9.5 deldir_2.0-2 +#> [153] Biostrings_2.70.2 sccore_1.0.4 +#> [155] splines_4.3.2 tensor_1.5 +#> [157] locfit_1.5-9.8 igraph_2.0.1.1 +#> [159] spatstat.geom_3.2-8 RcppHNSW_0.6.0 +#> [161] reshape2_1.4.4 ScaledMatrix_1.10.0 +#> [163] XML_3.99-0.16.1 BiocVersion_3.18.1 +#> [165] evaluate_0.23 golem_0.4.1 +#> [167] BiocManager_1.30.22 foreach_1.5.2 +#> [169] httpuv_1.6.14 RANN_2.6.1 +#> [171] tidyr_1.3.1 purrr_1.0.2 +#> [173] polyclip_1.10-6 benchmarkme_1.0.8 +#> [175] future_1.33.1 scattermore_1.2 +#> [177] rsvd_1.0.5 xtable_1.8-4 +#> [179] restfulr_0.0.15 RSpectra_0.16-1 +#> [181] later_1.3.2 viridisLite_0.4.2 +#> [183] ragg_1.2.7 tibble_3.2.1 +#> [185] GenomicAlignments_1.38.2 memoise_2.0.1 +#> [187] beeswarm_0.4.0 AnnotationDbi_1.64.1 +#> [189] cluster_2.1.6 shinyWidgets_0.8.1 +#> [191] globals_0.16.2
diff --git a/docs/articles/parameter-selection.html b/docs/articles/parameter-selection.html index 31d4c0a..4ea8a5f 100644 --- a/docs/articles/parameter-selection.html +++ b/docs/articles/parameter-selection.html @@ -33,7 +33,7 @@ Banksy - 0.99.9 + 0.99.12 @@ -344,7 +344,7 @@

Comparing cluster resultsSession information

Vignette runtime:

-
#> Time difference of 45.9482 secs
+
#> Time difference of 48.92457 secs
diff --git a/docs/index.html b/docs/index.html index 035c68d..8b8fb62 100644 --- a/docs/index.html +++ b/docs/index.html @@ -39,7 +39,7 @@ Banksy - 0.99.9 + 0.99.12 @@ -108,6 +108,7 @@

Overviewthe peer review file,
  • a tweetorial on BANKSY,
  • a set of vignettes showing basic usage,
    • +
  • usage compatibility with Seurat (here and here),
  • a Python version of this package,
  • a Zenodo archive containing scripts to reproduce the analyses in the paper, and the corresponding GitHub Pages (and here for analyses done in Python).
    • @@ -123,7 +124,7 @@

    Installationremotes::install_github("prabhakarlab/Banksy")

    To use the legacy version of Banksy utilising the BanksyObject class, use

    -remotes::install_github("prabhakarlab/Banksy@main")
    +remotes::install_github("prabhakarlab/Banksy@legacy")

    Banksy is also interoperable with Seurat via SeuratWrappers. Documentation on how to run BANKSY on Seurat objects can be found here. For installation of SeuratWrappers with BANKSY version >= 0.1.6, run

     remotes::install_github('satijalab/seurat-wrappers')
    @@ -238,7 +239,7 @@

    Quick start

    Runtime for analysis -
    #> Time difference of 57.72235 secs
    +
    #> Time difference of 57.44879 secs
    Session information diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 84b4003..f3ddea1 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 3.1.8 +pandoc: 3.1.13 pkgdown: 2.0.7 pkgdown_sha: ~ articles: @@ -6,7 +6,7 @@ articles: domain-segment: domain-segment.html multi-sample: multi-sample.html parameter-selection: parameter-selection.html -last_built: 2024-04-09T15:08Z +last_built: 2024-05-09T13:15Z urls: reference: https://prabhakarlab.github.io/Banksy/reference article: https://prabhakarlab.github.io/Banksy/articles diff --git a/docs/reference/Banksy-package.html b/docs/reference/Banksy-package.html index f0adca7..6b8de4f 100644 --- a/docs/reference/Banksy-package.html +++ b/docs/reference/Banksy-package.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/clusterBanksy.html b/docs/reference/clusterBanksy.html index a5d813e..2f674dd 100644 --- a/docs/reference/clusterBanksy.html +++ b/docs/reference/clusterBanksy.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/clusterNames.html b/docs/reference/clusterNames.html index 6a63e92..df6bb62 100644 --- a/docs/reference/clusterNames.html +++ b/docs/reference/clusterNames.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/compareClusters.html b/docs/reference/compareClusters.html index 033fbcd..be40e68 100644 --- a/docs/reference/compareClusters.html +++ b/docs/reference/compareClusters.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/computeBanksy.html b/docs/reference/computeBanksy.html index a304ebd..1969ac5 100644 --- a/docs/reference/computeBanksy.html +++ b/docs/reference/computeBanksy.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/connectClusters.html b/docs/reference/connectClusters.html index ba5bcf7..8f3f232 100644 --- a/docs/reference/connectClusters.html +++ b/docs/reference/connectClusters.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/getBanksyMatrix.html b/docs/reference/getBanksyMatrix.html index 2190999..9a0149b 100644 --- a/docs/reference/getBanksyMatrix.html +++ b/docs/reference/getBanksyMatrix.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/hippocampus.html b/docs/reference/hippocampus.html index 13fb45e..6cca402 100644 --- a/docs/reference/hippocampus.html +++ b/docs/reference/hippocampus.html @@ -21,7 +21,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/index.html b/docs/reference/index.html index f896b47..e657600 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/rings.html b/docs/reference/rings.html index 90c6dbf..9586079 100644 --- a/docs/reference/rings.html +++ b/docs/reference/rings.html @@ -18,7 +18,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/runBanksyPCA.html b/docs/reference/runBanksyPCA.html index f46faeb..3da0447 100644 --- a/docs/reference/runBanksyPCA.html +++ b/docs/reference/runBanksyPCA.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/runBanksyUMAP.html b/docs/reference/runBanksyUMAP.html index 04b8573..5afe626 100644 --- a/docs/reference/runBanksyUMAP.html +++ b/docs/reference/runBanksyUMAP.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/simulateDataset.html b/docs/reference/simulateDataset.html index 85fbbb4..7287b19 100644 --- a/docs/reference/simulateDataset.html +++ b/docs/reference/simulateDataset.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12 diff --git a/docs/reference/smoothLabels.html b/docs/reference/smoothLabels.html index 07785d0..8272df1 100644 --- a/docs/reference/smoothLabels.html +++ b/docs/reference/smoothLabels.html @@ -17,7 +17,7 @@ Banksy - 0.99.9 + 0.99.12