diff --git a/articles/MAGMA.Celltyping.html b/articles/MAGMA.Celltyping.html index 31c3781..71d9528 100644 --- a/articles/MAGMA.Celltyping.html +++ b/articles/MAGMA.Celltyping.html @@ -93,7 +93,7 @@


-Updated: Jul-15-2023
+Updated: Aug-20-2023

Source: vignettes/MAGMA.Celltyping.Rmd @@ -254,7 +254,7 @@

Merge results
 merged_results <- MAGMA.Celltyping::merge_results(
   MAGMA_results = MAGMA_results)
-
## Saving full merged results to ==> /tmp/Rtmp5qhvNk/MAGMA_celltyping./.lvl1.csv
+
## Saving full merged results to ==> /tmp/RtmpfhgSUF/MAGMA_celltyping./.lvl1.csv
 knitr::kable(merged_results)
@@ -934,7 +934,7 @@

Session Infoutils::sessionInfo() 
## R version 4.3.1 (2023-06-16)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 22.04.2 LTS
+## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -957,42 +957,42 @@ 
Session Info## other attached packages:
 ## [1] ewceData_1.9.0          ExperimentHub_2.9.1     AnnotationHub_3.9.1    
 ## [4] BiocFileCache_2.9.1     dbplyr_2.3.3            BiocGenerics_0.47.0    
-## [7] dplyr_1.1.2             MAGMA.Celltyping_2.0.11 BiocStyle_2.29.0       
+## [7] dplyr_1.1.2             MAGMA.Celltyping_2.0.11 BiocStyle_2.29.1       
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] splines_4.3.1                 later_1.3.1                  
 ##   [3] BiocIO_1.11.0                 bitops_1.0-7                 
-##   [5] ggplotify_0.1.1               filelock_1.0.2               
+##   [5] ggplotify_0.1.2               filelock_1.0.2               
 ##   [7] tibble_3.2.1                  R.oo_1.25.0                  
 ##   [9] XML_3.99-0.14                 lifecycle_1.0.3              
 ##  [11] rstatix_0.7.2                 rprojroot_2.0.3              
 ##  [13] MASS_7.3-60                   lattice_0.21-8               
 ##  [15] backports_1.4.1               magrittr_2.0.3               
-##  [17] limma_3.57.6                  plotly_4.10.2                
-##  [19] sass_0.4.7                    rmarkdown_2.23               
+##  [17] limma_3.57.7                  plotly_4.10.2                
+##  [19] sass_0.4.7                    rmarkdown_2.24               
 ##  [21] jquerylib_0.1.4               yaml_2.3.7                   
 ##  [23] httpuv_1.6.11                 HGNChelper_0.8.1             
 ##  [25] minqa_1.2.5                   DBI_1.1.3                    
 ##  [27] abind_1.4-5                   zlibbioc_1.47.0              
-##  [29] GenomicRanges_1.53.1          purrr_1.0.1                  
+##  [29] GenomicRanges_1.53.1          purrr_1.0.2                  
 ##  [31] R.utils_2.12.2                RCurl_1.98-1.12              
-##  [33] yulab.utils_0.0.6             VariantAnnotation_1.47.1     
+##  [33] yulab.utils_0.0.7             VariantAnnotation_1.47.1     
 ##  [35] rappdirs_0.3.3                GenomeInfoDbData_1.2.10      
 ##  [37] IRanges_2.35.2                S4Vectors_0.39.1             
-##  [39] tidytree_0.4.4                pkgdown_2.0.7                
-##  [41] codetools_0.2-19              DelayedArray_0.27.9          
+##  [39] tidytree_0.4.5                pkgdown_2.0.7                
+##  [41] codetools_0.2-19              DelayedArray_0.27.10         
 ##  [43] xml2_1.3.5                    tidyselect_1.2.0             
-##  [45] aplot_0.1.10                  farver_2.1.1                 
+##  [45] aplot_0.2.0                   farver_2.1.1                 
 ##  [47] lme4_1.1-34                   matrixStats_1.0.0            
 ##  [49] stats4_4.3.1                  GenomicAlignments_1.37.0     
 ##  [51] jsonlite_1.8.7                ellipsis_0.3.2               
 ##  [53] systemfonts_1.0.4             tools_4.3.1                  
-##  [55] progress_1.2.2                treeio_1.25.1                
+##  [55] progress_1.2.2                treeio_1.25.3                
 ##  [57] ragg_1.2.5                    Rcpp_1.0.11                  
-##  [59] glue_1.6.2                    SparseArray_1.1.10           
-##  [61] xfun_0.39                     MatrixGenerics_1.13.0        
+##  [59] glue_1.6.2                    SparseArray_1.1.11           
+##  [61] xfun_0.40                     MatrixGenerics_1.13.1        
 ##  [63] GenomeInfoDb_1.37.2           RNOmni_1.0.1                 
-##  [65] withr_2.5.0                   BiocManager_1.30.21          
+##  [65] withr_2.5.0                   BiocManager_1.30.22          
 ##  [67] fastmap_1.1.1                 boot_1.3-28.1                
 ##  [69] fansi_1.0.4                   digest_0.6.33                
 ##  [71] R6_2.5.1                      mime_0.12                    
@@ -1001,24 +1001,24 @@ 
Session Info##  [77] RSQLite_2.3.1                 R.methodsS3_1.8.2            
 ##  [79] utf8_1.2.3                    tidyr_1.3.0                  
 ##  [81] generics_0.1.3                data.table_1.14.8            
-##  [83] rtracklayer_1.61.0            prettyunits_1.1.1            
-##  [85] httr_1.4.6                    htmlwidgets_1.6.2            
-##  [87] S4Arrays_1.1.4                pkgconfig_2.0.3              
+##  [83] rtracklayer_1.61.1            prettyunits_1.1.1            
+##  [85] httr_1.4.7                    htmlwidgets_1.6.2            
+##  [87] S4Arrays_1.1.5                pkgconfig_2.0.3              
 ##  [89] gtable_0.3.3                  blob_1.2.4                   
 ##  [91] SingleCellExperiment_1.23.0   XVector_0.41.1               
-##  [93] htmltools_0.5.5               carData_3.0-5                
-##  [95] bookdown_0.34                 scales_1.2.1                 
+##  [93] htmltools_0.5.6               carData_3.0-5                
+##  [95] bookdown_0.35                 scales_1.2.1                 
 ##  [97] Biobase_2.61.0                png_0.1-8                    
-##  [99] ggdendro_0.1.23               ggfun_0.1.1                  
+##  [99] ggdendro_0.1.23               ggfun_0.1.2                  
 ## [101] knitr_1.43                    reshape2_1.4.4               
 ## [103] rjson_0.2.21                  nloptr_2.0.3                 
-## [105] nlme_3.1-162                  curl_5.0.1                   
+## [105] nlme_3.1-163                  curl_5.0.2                   
 ## [107] cachem_1.0.8                  stringr_1.5.0                
 ## [109] BiocVersion_3.18.0            parallel_4.3.1               
 ## [111] AnnotationDbi_1.63.2          restfulr_0.0.15              
 ## [113] desc_1.4.2                    pillar_1.9.0                 
 ## [115] grid_4.3.1                    vctrs_0.6.3                  
-## [117] promises_1.2.0.1              ggpubr_0.6.0                 
+## [117] promises_1.2.1                ggpubr_0.6.0                 
 ## [119] car_3.1-2                     xtable_1.8-4                 
 ## [121] evaluate_0.21                 orthogene_1.7.0              
 ## [123] GenomicFeatures_1.53.1        cli_3.6.1                    
@@ -1027,22 +1027,22 @@ 
Session Info## [129] grr_0.9.5                     ggsignif_0.6.4               
 ## [131] labeling_0.4.2                gprofiler2_0.2.2             
 ## [133] EWCE_1.9.2                    plyr_1.8.8                   
-## [135] fs_1.6.2                      stringi_1.7.12               
-## [137] viridisLite_0.4.2             BiocParallel_1.35.3          
+## [135] fs_1.6.3                      stringi_1.7.12               
+## [137] viridisLite_0.4.2             BiocParallel_1.35.4          
 ## [139] assertthat_0.2.1              babelgene_22.9               
 ## [141] munsell_0.5.0                 Biostrings_2.69.2            
 ## [143] gh_1.4.0                      lazyeval_0.2.2               
-## [145] homologene_1.4.68.19.3.27     Matrix_1.6-0                 
-## [147] MungeSumstats_1.9.11          BSgenome_1.69.0              
-## [149] hms_1.1.3                     patchwork_1.1.2              
-## [151] bit64_4.0.5                   ggplot2_3.4.2                
-## [153] KEGGREST_1.41.0               shiny_1.7.4.1                
-## [155] highr_0.10                    SummarizedExperiment_1.31.1  
-## [157] interactiveDisplayBase_1.39.0 googleAuthR_2.0.1            
-## [159] gargle_1.5.1                  broom_1.0.5                  
-## [161] memoise_2.0.1                 bslib_0.5.0                  
-## [163] ggtree_3.9.0                  bit_4.0.5                    
-## [165] ape_5.7-1
+## [145] homologene_1.4.68.19.3.27 Matrix_1.6-1 +## [147] MungeSumstats_1.9.15 BSgenome_1.69.0 +## [149] hms_1.1.3 patchwork_1.1.3 +## [151] bit64_4.0.5 ggplot2_3.4.3 +## [153] KEGGREST_1.41.0 statmod_1.5.0 +## [155] shiny_1.7.5 highr_0.10 +## [157] SummarizedExperiment_1.31.1 interactiveDisplayBase_1.39.0 +## [159] googleAuthR_2.0.1 gargle_1.5.2 +## [161] broom_1.0.5 memoise_2.0.1 +## [163] bslib_0.5.1 ggtree_3.9.1 +## [165] bit_4.0.5 ape_5.7-1
diff --git a/articles/docker.html b/articles/docker.html index 4efcca4..66f46b6 100644 --- a/articles/docker.html +++ b/articles/docker.html @@ -93,7 +93,7 @@


-Vignette updated: Jul-15-2023
+Vignette updated: Aug-20-2023

Source: vignettes/docker.Rmd @@ -173,7 +173,7 @@

Session Infoutils::sessionInfo() 
## R version 4.3.1 (2023-06-16)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 22.04.2 LTS
+## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -194,43 +194,43 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] MAGMA.Celltyping_2.0.11 BiocStyle_2.29.0       
+## [1] MAGMA.Celltyping_2.0.11 BiocStyle_2.29.1       
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] splines_4.3.1                 later_1.3.1                  
 ##   [3] BiocIO_1.11.0                 bitops_1.0-7                 
-##   [5] ggplotify_0.1.1               filelock_1.0.2               
+##   [5] ggplotify_0.1.2               filelock_1.0.2               
 ##   [7] tibble_3.2.1                  R.oo_1.25.0                  
 ##   [9] XML_3.99-0.14                 lifecycle_1.0.3              
 ##  [11] rstatix_0.7.2                 rprojroot_2.0.3              
 ##  [13] MASS_7.3-60                   lattice_0.21-8               
 ##  [15] backports_1.4.1               magrittr_2.0.3               
-##  [17] limma_3.57.6                  plotly_4.10.2                
-##  [19] sass_0.4.7                    rmarkdown_2.23               
+##  [17] limma_3.57.7                  plotly_4.10.2                
+##  [19] sass_0.4.7                    rmarkdown_2.24               
 ##  [21] jquerylib_0.1.4               yaml_2.3.7                   
 ##  [23] httpuv_1.6.11                 HGNChelper_0.8.1             
 ##  [25] minqa_1.2.5                   DBI_1.1.3                    
 ##  [27] abind_1.4-5                   zlibbioc_1.47.0              
-##  [29] GenomicRanges_1.53.1          purrr_1.0.1                  
+##  [29] GenomicRanges_1.53.1          purrr_1.0.2                  
 ##  [31] R.utils_2.12.2                BiocGenerics_0.47.0          
-##  [33] RCurl_1.98-1.12               yulab.utils_0.0.6            
+##  [33] RCurl_1.98-1.12               yulab.utils_0.0.7            
 ##  [35] VariantAnnotation_1.47.1      rappdirs_0.3.3               
 ##  [37] GenomeInfoDbData_1.2.10       IRanges_2.35.2               
-##  [39] S4Vectors_0.39.1              tidytree_0.4.4               
+##  [39] S4Vectors_0.39.1              tidytree_0.4.5               
 ##  [41] pkgdown_2.0.7                 codetools_0.2-19             
-##  [43] DelayedArray_0.27.9           xml2_1.3.5                   
-##  [45] tidyselect_1.2.0              aplot_0.1.10                 
+##  [43] DelayedArray_0.27.10          xml2_1.3.5                   
+##  [45] tidyselect_1.2.0              aplot_0.2.0                  
 ##  [47] lme4_1.1-34                   matrixStats_1.0.0            
 ##  [49] stats4_4.3.1                  BiocFileCache_2.9.1          
 ##  [51] GenomicAlignments_1.37.0      jsonlite_1.8.7               
 ##  [53] ellipsis_0.3.2                systemfonts_1.0.4            
 ##  [55] tools_4.3.1                   progress_1.2.2               
-##  [57] treeio_1.25.1                 ragg_1.2.5                   
+##  [57] treeio_1.25.3                 ragg_1.2.5                   
 ##  [59] Rcpp_1.0.11                   glue_1.6.2                   
-##  [61] SparseArray_1.1.10            xfun_0.39                    
-##  [63] MatrixGenerics_1.13.0         GenomeInfoDb_1.37.2          
+##  [61] SparseArray_1.1.11            xfun_0.40                    
+##  [63] MatrixGenerics_1.13.1         GenomeInfoDb_1.37.2          
 ##  [65] RNOmni_1.0.1                  dplyr_1.1.2                  
-##  [67] BiocManager_1.30.21           fastmap_1.1.1                
+##  [67] BiocManager_1.30.22           fastmap_1.1.1                
 ##  [69] boot_1.3-28.1                 fansi_1.0.4                  
 ##  [71] digest_0.6.33                 R6_2.5.1                     
 ##  [73] mime_0.12                     gridGraphics_0.5-1           
@@ -238,24 +238,24 @@ 
Session Info##  [77] biomaRt_2.57.1                RSQLite_2.3.1                
 ##  [79] R.methodsS3_1.8.2             utf8_1.2.3                   
 ##  [81] tidyr_1.3.0                   generics_0.1.3               
-##  [83] data.table_1.14.8             rtracklayer_1.61.0           
-##  [85] prettyunits_1.1.1             httr_1.4.6                   
-##  [87] htmlwidgets_1.6.2             S4Arrays_1.1.4               
+##  [83] data.table_1.14.8             rtracklayer_1.61.1           
+##  [85] prettyunits_1.1.1             httr_1.4.7                   
+##  [87] htmlwidgets_1.6.2             S4Arrays_1.1.5               
 ##  [89] pkgconfig_2.0.3               gtable_0.3.3                 
 ##  [91] blob_1.2.4                    SingleCellExperiment_1.23.0  
-##  [93] XVector_0.41.1                htmltools_0.5.5              
-##  [95] carData_3.0-5                 bookdown_0.34                
+##  [93] XVector_0.41.1                htmltools_0.5.6              
+##  [95] carData_3.0-5                 bookdown_0.35                
 ##  [97] scales_1.2.1                  Biobase_2.61.0               
 ##  [99] png_0.1-8                     ggdendro_0.1.23              
-## [101] ggfun_0.1.1                   knitr_1.43                   
+## [101] ggfun_0.1.2                   knitr_1.43                   
 ## [103] reshape2_1.4.4                rjson_0.2.21                 
-## [105] nloptr_2.0.3                  nlme_3.1-162                 
-## [107] curl_5.0.1                    cachem_1.0.8                 
+## [105] nloptr_2.0.3                  nlme_3.1-163                 
+## [107] curl_5.0.2                    cachem_1.0.8                 
 ## [109] stringr_1.5.0                 BiocVersion_3.18.0           
 ## [111] parallel_4.3.1                AnnotationDbi_1.63.2         
 ## [113] restfulr_0.0.15               desc_1.4.2                   
 ## [115] pillar_1.9.0                  grid_4.3.1                   
-## [117] vctrs_0.6.3                   promises_1.2.0.1             
+## [117] vctrs_0.6.3                   promises_1.2.1               
 ## [119] ggpubr_0.6.0                  car_3.1-2                    
 ## [121] dbplyr_2.3.3                  xtable_1.8-4                 
 ## [123] evaluate_0.21                 orthogene_1.7.0              
@@ -264,23 +264,24 @@ 
Session Info## [129] rlang_1.1.1                   crayon_1.5.2                 
 ## [131] grr_0.9.5                     ggsignif_0.6.4               
 ## [133] gprofiler2_0.2.2              EWCE_1.9.2                   
-## [135] plyr_1.8.8                    fs_1.6.2                     
+## [135] plyr_1.8.8                    fs_1.6.3                     
 ## [137] stringi_1.7.12                viridisLite_0.4.2            
-## [139] ewceData_1.9.0                BiocParallel_1.35.3          
+## [139] ewceData_1.9.0                BiocParallel_1.35.4          
 ## [141] assertthat_0.2.1              babelgene_22.9               
 ## [143] munsell_0.5.0                 Biostrings_2.69.2            
 ## [145] gh_1.4.0                      lazyeval_0.2.2               
-## [147] homologene_1.4.68.19.3.27     Matrix_1.6-0                 
-## [149] ExperimentHub_2.9.1           MungeSumstats_1.9.11         
+## [147] homologene_1.4.68.19.3.27     Matrix_1.6-1                 
+## [149] ExperimentHub_2.9.1           MungeSumstats_1.9.15         
 ## [151] BSgenome_1.69.0               hms_1.1.3                    
-## [153] patchwork_1.1.2               bit64_4.0.5                  
-## [155] ggplot2_3.4.2                 KEGGREST_1.41.0              
-## [157] shiny_1.7.4.1                 SummarizedExperiment_1.31.1  
-## [159] interactiveDisplayBase_1.39.0 AnnotationHub_3.9.1          
-## [161] googleAuthR_2.0.1             gargle_1.5.1                 
-## [163] broom_1.0.5                   memoise_2.0.1                
-## [165] bslib_0.5.0                   ggtree_3.9.0                 
-## [167] bit_4.0.5                     ape_5.7-1
+## [153] patchwork_1.1.3 bit64_4.0.5 +## [155] ggplot2_3.4.3 KEGGREST_1.41.0 +## [157] statmod_1.5.0 shiny_1.7.5 +## [159] SummarizedExperiment_1.31.1 interactiveDisplayBase_1.39.0 +## [161] AnnotationHub_3.9.1 googleAuthR_2.0.1 +## [163] gargle_1.5.2 broom_1.0.5 +## [165] memoise_2.0.1 bslib_0.5.1 +## [167] ggtree_3.9.1 bit_4.0.5 +## [169] ape_5.7-1


diff --git a/articles/full_workflow.html b/articles/full_workflow.html index 854406d..667046d 100644 --- a/articles/full_workflow.html +++ b/articles/full_workflow.html @@ -93,7 +93,7 @@


-Updated: Jul-15-2023
+Updated: Aug-20-2023

Source: vignettes/full_workflow.Rmd @@ -595,7 +595,7 @@

Session Infoutils::sessionInfo() 
## R version 4.3.1 (2023-06-16)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 22.04.2 LTS
+## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -616,42 +616,42 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] dplyr_1.1.2             MAGMA.Celltyping_2.0.11 BiocStyle_2.29.0       
+## [1] dplyr_1.1.2             MAGMA.Celltyping_2.0.11 BiocStyle_2.29.1       
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] splines_4.3.1                 later_1.3.1                  
 ##   [3] BiocIO_1.11.0                 bitops_1.0-7                 
-##   [5] ggplotify_0.1.1               filelock_1.0.2               
+##   [5] ggplotify_0.1.2               filelock_1.0.2               
 ##   [7] tibble_3.2.1                  R.oo_1.25.0                  
 ##   [9] XML_3.99-0.14                 lifecycle_1.0.3              
 ##  [11] rstatix_0.7.2                 rprojroot_2.0.3              
 ##  [13] MASS_7.3-60                   lattice_0.21-8               
 ##  [15] backports_1.4.1               magrittr_2.0.3               
-##  [17] limma_3.57.6                  plotly_4.10.2                
-##  [19] sass_0.4.7                    rmarkdown_2.23               
+##  [17] limma_3.57.7                  plotly_4.10.2                
+##  [19] sass_0.4.7                    rmarkdown_2.24               
 ##  [21] jquerylib_0.1.4               yaml_2.3.7                   
 ##  [23] httpuv_1.6.11                 HGNChelper_0.8.1             
 ##  [25] minqa_1.2.5                   DBI_1.1.3                    
 ##  [27] abind_1.4-5                   zlibbioc_1.47.0              
-##  [29] GenomicRanges_1.53.1          purrr_1.0.1                  
+##  [29] GenomicRanges_1.53.1          purrr_1.0.2                  
 ##  [31] R.utils_2.12.2                BiocGenerics_0.47.0          
-##  [33] RCurl_1.98-1.12               yulab.utils_0.0.6            
+##  [33] RCurl_1.98-1.12               yulab.utils_0.0.7            
 ##  [35] VariantAnnotation_1.47.1      rappdirs_0.3.3               
 ##  [37] GenomeInfoDbData_1.2.10       IRanges_2.35.2               
-##  [39] S4Vectors_0.39.1              tidytree_0.4.4               
+##  [39] S4Vectors_0.39.1              tidytree_0.4.5               
 ##  [41] pkgdown_2.0.7                 codetools_0.2-19             
-##  [43] DelayedArray_0.27.9           xml2_1.3.5                   
-##  [45] tidyselect_1.2.0              aplot_0.1.10                 
+##  [43] DelayedArray_0.27.10          xml2_1.3.5                   
+##  [45] tidyselect_1.2.0              aplot_0.2.0                  
 ##  [47] lme4_1.1-34                   matrixStats_1.0.0            
 ##  [49] stats4_4.3.1                  BiocFileCache_2.9.1          
 ##  [51] GenomicAlignments_1.37.0      jsonlite_1.8.7               
 ##  [53] ellipsis_0.3.2                systemfonts_1.0.4            
 ##  [55] tools_4.3.1                   progress_1.2.2               
-##  [57] treeio_1.25.1                 ragg_1.2.5                   
+##  [57] treeio_1.25.3                 ragg_1.2.5                   
 ##  [59] Rcpp_1.0.11                   glue_1.6.2                   
-##  [61] SparseArray_1.1.10            xfun_0.39                    
-##  [63] MatrixGenerics_1.13.0         GenomeInfoDb_1.37.2          
-##  [65] RNOmni_1.0.1                  BiocManager_1.30.21          
+##  [61] SparseArray_1.1.11            xfun_0.40                    
+##  [63] MatrixGenerics_1.13.1         GenomeInfoDb_1.37.2          
+##  [65] RNOmni_1.0.1                  BiocManager_1.30.22          
 ##  [67] fastmap_1.1.1                 boot_1.3-28.1                
 ##  [69] fansi_1.0.4                   digest_0.6.33                
 ##  [71] R6_2.5.1                      mime_0.12                    
@@ -660,24 +660,24 @@ 
Session Info##  [77] RSQLite_2.3.1                 R.methodsS3_1.8.2            
 ##  [79] utf8_1.2.3                    tidyr_1.3.0                  
 ##  [81] generics_0.1.3                data.table_1.14.8            
-##  [83] rtracklayer_1.61.0            prettyunits_1.1.1            
-##  [85] httr_1.4.6                    htmlwidgets_1.6.2            
-##  [87] S4Arrays_1.1.4                pkgconfig_2.0.3              
+##  [83] rtracklayer_1.61.1            prettyunits_1.1.1            
+##  [85] httr_1.4.7                    htmlwidgets_1.6.2            
+##  [87] S4Arrays_1.1.5                pkgconfig_2.0.3              
 ##  [89] gtable_0.3.3                  blob_1.2.4                   
 ##  [91] SingleCellExperiment_1.23.0   XVector_0.41.1               
-##  [93] htmltools_0.5.5               carData_3.0-5                
-##  [95] bookdown_0.34                 scales_1.2.1                 
+##  [93] htmltools_0.5.6               carData_3.0-5                
+##  [95] bookdown_0.35                 scales_1.2.1                 
 ##  [97] Biobase_2.61.0                png_0.1-8                    
-##  [99] ggdendro_0.1.23               ggfun_0.1.1                  
+##  [99] ggdendro_0.1.23               ggfun_0.1.2                  
 ## [101] knitr_1.43                    reshape2_1.4.4               
 ## [103] rjson_0.2.21                  nloptr_2.0.3                 
-## [105] nlme_3.1-162                  curl_5.0.1                   
+## [105] nlme_3.1-163                  curl_5.0.2                   
 ## [107] cachem_1.0.8                  stringr_1.5.0                
 ## [109] BiocVersion_3.18.0            parallel_4.3.1               
 ## [111] AnnotationDbi_1.63.2          restfulr_0.0.15              
 ## [113] desc_1.4.2                    pillar_1.9.0                 
 ## [115] grid_4.3.1                    vctrs_0.6.3                  
-## [117] promises_1.2.0.1              ggpubr_0.6.0                 
+## [117] promises_1.2.1                ggpubr_0.6.0                 
 ## [119] car_3.1-2                     dbplyr_2.3.3                 
 ## [121] xtable_1.8-4                  evaluate_0.21                
 ## [123] orthogene_1.7.0               GenomicFeatures_1.53.1       
@@ -686,23 +686,23 @@ 
Session Info## [129] crayon_1.5.2                  grr_0.9.5                    
 ## [131] ggsignif_0.6.4                gprofiler2_0.2.2             
 ## [133] EWCE_1.9.2                    plyr_1.8.8                   
-## [135] fs_1.6.2                      stringi_1.7.12               
+## [135] fs_1.6.3                      stringi_1.7.12               
 ## [137] viridisLite_0.4.2             ewceData_1.9.0               
-## [139] BiocParallel_1.35.3           assertthat_0.2.1             
+## [139] BiocParallel_1.35.4           assertthat_0.2.1             
 ## [141] babelgene_22.9                munsell_0.5.0                
 ## [143] Biostrings_2.69.2             gh_1.4.0                     
 ## [145] lazyeval_0.2.2                homologene_1.4.68.19.3.27    
-## [147] Matrix_1.6-0                  ExperimentHub_2.9.1          
-## [149] MungeSumstats_1.9.11          BSgenome_1.69.0              
-## [151] hms_1.1.3                     patchwork_1.1.2              
-## [153] bit64_4.0.5                   ggplot2_3.4.2                
-## [155] KEGGREST_1.41.0               shiny_1.7.4.1                
-## [157] SummarizedExperiment_1.31.1   interactiveDisplayBase_1.39.0
-## [159] AnnotationHub_3.9.1           googleAuthR_2.0.1            
-## [161] gargle_1.5.1                  broom_1.0.5                  
-## [163] memoise_2.0.1                 bslib_0.5.0                  
-## [165] ggtree_3.9.0                  bit_4.0.5                    
-## [167] ape_5.7-1
+## [147] Matrix_1.6-1 ExperimentHub_2.9.1 +## [149] MungeSumstats_1.9.15 BSgenome_1.69.0 +## [151] hms_1.1.3 patchwork_1.1.3 +## [153] bit64_4.0.5 ggplot2_3.4.3 +## [155] KEGGREST_1.41.0 statmod_1.5.0 +## [157] shiny_1.7.5 SummarizedExperiment_1.31.1 +## [159] interactiveDisplayBase_1.39.0 AnnotationHub_3.9.1 +## [161] googleAuthR_2.0.1 gargle_1.5.2 +## [163] broom_1.0.5 memoise_2.0.1 +## [165] bslib_0.5.1 ggtree_3.9.1 +## [167] bit_4.0.5 ape_5.7-1 diff --git a/index.html b/index.html index c715ef6..5fd4023 100644 --- a/index.html +++ b/index.html @@ -89,7 +89,7 @@ Authors: Brian Schilder, Alan Murphy, Julien Bryois, Nathan Skene

-README updated: Jul-15-2023 +README updated: Aug-20-2023

Introduction diff --git a/news/index.html b/news/index.html index 7383406..af16cd1 100644 --- a/news/index.html +++ b/news/index.html @@ -66,6 +66,13 @@

Changelog

MAGMA.Celltyping 2.0.11

+

New features

+
  • +map_snps_to_genes: +
    • expose storage_dir arg to check_genomeLocFile.
      • +
    • +
+

Bug fixes

  • create_fake_gwas_path @@ -76,6 +83,10 @@

    Bug fixes +

    Bug fixes

    +
    • Fix GHA downloads with “libcurl” settings.
      • +

MAGMA.Celltyping 2.0.10

diff --git a/pkgdown.yml b/pkgdown.yml index 98db232..2f46330 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,5 +5,5 @@ articles: MAGMA.Celltyping: MAGMA.Celltyping.html docker: docker.html full_workflow: full_workflow.html -last_built: 2023-07-15T18:07Z +last_built: 2023-08-20T12:10Z diff --git a/reference/calculate_conditional_celltype_associations.html b/reference/calculate_conditional_celltype_associations.html index 453bb01..c584462 100644 --- a/reference/calculate_conditional_celltype_associations.html +++ b/reference/calculate_conditional_celltype_associations.html @@ -256,29 +256,29 @@

Examples

#> Mapping gene symbols in specificity_quantiles matrix to entrez IDs. #> Mapping gene symbols in specificity_quantiles matrix to entrez IDs. #> magma -#> --gene-results '/tmp/RtmpaAQYbg/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' -#> --gene-covar '/tmp/RtmpaAQYbg/file1a0769481715' +#> --gene-results '/tmp/RtmpvpvoXN/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' +#> --gene-covar '/tmp/RtmpvpvoXN/file1c485bf457de' #> --model direction=pos condition='oligodendrocytes' -#> --out '/tmp/RtmpaAQYbg/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level1.35UP.10DOWN.Linear.ControlFor_oligodendrocytes' +#> --out '/tmp/RtmpvpvoXN/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level1.35UP.10DOWN.Linear.ControlFor_oligodendrocytes' #> Reading enrichment results file into R. #> magma -#> --gene-results '/tmp/RtmpaAQYbg/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' -#> --gene-covar '/tmp/RtmpaAQYbg/file1a0769481715' +#> --gene-results '/tmp/RtmpvpvoXN/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' +#> --gene-covar '/tmp/RtmpvpvoXN/file1c485bf457de' #> --model direction=pos condition='oligodendrocytes' -#> --out '/tmp/RtmpaAQYbg/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level1.35UP.10DOWN.ControlFor_oligodendrocytes' +#> --out '/tmp/RtmpvpvoXN/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level1.35UP.10DOWN.ControlFor_oligodendrocytes' #> Reading enrichment results file into R. #> Mapping gene symbols in specificity_quantiles matrix to entrez IDs. #> magma -#> --gene-results '/tmp/RtmpaAQYbg/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' -#> --gene-covar '/tmp/RtmpaAQYbg/file1a074f9c3113' +#> --gene-results '/tmp/RtmpvpvoXN/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' +#> --gene-covar '/tmp/RtmpvpvoXN/file1c48bb92f5d' #> --model direction=pos condition='oligodendrocytes' -#> --out '/tmp/RtmpaAQYbg/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level2.35UP.10DOWN.Linear.ControlFor_oligodendrocytes' +#> --out '/tmp/RtmpvpvoXN/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level2.35UP.10DOWN.Linear.ControlFor_oligodendrocytes' #> Reading enrichment results file into R. #> magma -#> --gene-results '/tmp/RtmpaAQYbg/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' -#> --gene-covar '/tmp/RtmpaAQYbg/file1a074f9c3113' +#> --gene-results '/tmp/RtmpvpvoXN/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' +#> --gene-covar '/tmp/RtmpvpvoXN/file1c48bb92f5d' #> --model direction=pos condition='oligodendrocytes' -#> --out '/tmp/RtmpaAQYbg/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level2.35UP.10DOWN.ControlFor_oligodendrocytes' +#> --out '/tmp/RtmpvpvoXN/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level2.35UP.10DOWN.ControlFor_oligodendrocytes' #> Reading enrichment results file into R.
diff --git a/reference/celltype_associations_pipeline.html b/reference/celltype_associations_pipeline.html index d515662..4164db7 100644 --- a/reference/celltype_associations_pipeline.html +++ b/reference/celltype_associations_pipeline.html @@ -247,7 +247,7 @@

Examples

#> Constructing top10% gene marker sets for 8 cell-types.#> Reading enrichment results file into R.#> Merging linear and top10% results -#> Saving results ==> /tmp/RtmpaAQYbg/Zeisel2015/MAGMA_celltyping.Zeisel2015.rds +#> Saving results ==> /tmp/RtmpvpvoXN/Zeisel2015/MAGMA_celltyping.Zeisel2015.rds diff --git a/reference/create_DT.html b/reference/create_DT.html index f64109e..bdf4e33 100644 --- a/reference/create_DT.html +++ b/reference/create_DT.html @@ -100,8 +100,8 @@

Examples

data("mtcars")
 create_DT(mtcars)
 #> Loading required namespace: DT
-

-
+
+