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• 19:21, 6 December 2025 Brb talk contribs created page File:Youtube-embed.png
• 19:21, 6 December 2025 Brb talk contribs uploaded File:Youtube-embed.png
• 10:48, 1 December 2025 Brb talk contribs created page File:Dendro colorbars.png (<syntaxhighlight lang='r'> library(ComplexHeatmap) library(circlize) library(RColorBrewer) set.seed(123) # --- Example data (10 samples) --- mat <- matrix(rnorm(30), nrow = 10) rownames(mat) <- paste0("Sample", 1:10) mat[1:5, ] <- mat[1:5, ] mat[6:10, ] <- mat[6:10, ] + 2 # Cluster on samples (rows) hc <- hclust(dist(mat)) # Annotations in ORIGINAL sample order groups <- rep(c("A", "B"), each = 5) score <- seq(0, 1, length = 10) cl2 <- cutree(hc, 2) cl3 <- cutree(hc, 3) cl4 <- cutree(hc,...)
• 10:48, 1 December 2025 Brb talk contribs uploaded File:Dendro colorbars.png (<syntaxhighlight lang='r'> library(ComplexHeatmap) library(circlize) library(RColorBrewer) set.seed(123) # --- Example data (10 samples) --- mat <- matrix(rnorm(30), nrow = 10) rownames(mat) <- paste0("Sample", 1:10) mat[1:5, ] <- mat[1:5, ] mat[6:10, ] <- mat[6:10, ] + 2 # Cluster on samples (rows) hc <- hclust(dist(mat)) # Annotations in ORIGINAL sample order groups <- rep(c("A", "B"), each = 5) score <- seq(0, 1, length = 10) cl2 <- cutree(hc, 2) cl3 <- cutree(hc, 3) cl4 <- cutree(hc,...)
• 17:16, 10 November 2025 Brb talk contribs created page File:Umap-iris.png (<syntaxhighlight lang='r'> library(umap) # Load the built-in Iris dataset data(iris) # Separate the features (variables) from the species labels iris_features <- iris[, 1:4] iris_species <- iris[, 5] # Run UMAP, reducing the 4 dimensions down to 2 # n_neighbors: Controls how UMAP balances local vs. global structure. # min_dist: Controls how tightly points are packed together. iris_umap_results <- umap(iris_features, random_state = 42) # The result is a list. The actual 2D coordinates are...)
• 17:16, 10 November 2025 Brb talk contribs uploaded File:Umap-iris.png (<syntaxhighlight lang='r'> library(umap) # Load the built-in Iris dataset data(iris) # Separate the features (variables) from the species labels iris_features <- iris[, 1:4] iris_species <- iris[, 5] # Run UMAP, reducing the 4 dimensions down to 2 # n_neighbors: Controls how UMAP balances local vs. global structure. # min_dist: Controls how tightly points are packed together. iris_umap_results <- umap(iris_features, random_state = 42) # The result is a list. The actual 2D coordinates are...)
• 19:07, 28 October 2025 Brb talk contribs created page File:Paletteer d.png (<syntaxhighlight lang='r'> paletteer_d("RColorBrewer::RdBu") #<colors> #67001FFF #B2182BFF #D6604DFF #F4A582FF #FDDBC7FF #F7F7F7FF #D1E5F0FF #92C5DEFF #4393C3FF #2166ACFF #053061FF paletteer_d("ggsci::uniform_startrek") # <colors> #CC0C00FF #5C88DAFF #84BD00FF #FFCD00FF #7C878EFF #00B5E2FF #00AF66FF </syntaxhighlight>)
• 19:07, 28 October 2025 Brb talk contribs uploaded File:Paletteer d.png (<syntaxhighlight lang='r'> paletteer_d("RColorBrewer::RdBu") #<colors> #67001FFF #B2182BFF #D6604DFF #F4A582FF #FDDBC7FF #F7F7F7FF #D1E5F0FF #92C5DEFF #4393C3FF #2166ACFF #053061FF paletteer_d("ggsci::uniform_startrek") # <colors> #CC0C00FF #5C88DAFF #84BD00FF #FFCD00FF #7C878EFF #00B5E2FF #00AF66FF </syntaxhighlight>)
• 11:26, 9 October 2025 Brb talk contribs created page Mediawiki-docker (Created page with "= Directories = * Backup directory '''~/backups''' * Mediawiki directory '''~/mediawiki-docker''' = Accounts = * Note the mediawiki admin and user accounts are embedded in the SQL database. * DB account (defined in compose.yml and LocalSettings.php): ** database: wikidb ($wgDBname) ** user: ($wgDBuser) ** password: ($wgDBpassword) * Mediawiki admin: * Mediawiki user: = Backup = Assume the mediawiki directory on the host is '''/var/www/html/wiki''' <ul> <li>MySQL <...")
• 15:12, 4 October 2025 Brb talk contribs created page File:Massage.png
• 15:12, 4 October 2025 Brb talk contribs uploaded File:Massage.png
• 14:57, 8 September 2025 Brb talk contribs created page File:MacSettingKeyboardShortcut.png
• 14:57, 8 September 2025 Brb talk contribs uploaded File:MacSettingKeyboardShortcut.png
• 14:56, 8 September 2025 Brb talk contribs created page File:MacSettingLiveCaption.png
• 14:56, 8 September 2025 Brb talk contribs uploaded File:MacSettingLiveCaption.png
• 09:17, 7 August 2025 Brb talk contribs created page File:Heatmap-gaps.png (<syntaxhighlight lang='r'> # 1. Prepare the data set.seed(42) mat = matrix(rnorm(30, mean = 0, sd = 1.2), nrow = 5, ncol = 6) mat[2, 1] = -2.5 mat[2, 6] = 2.5 mat[1, 2] = -1.8 mat[4, 4] = 1.8 # 2. Define the color palette library(circlize) col_fun = colorRamp2(c(-2.5, 0, 2.5), c("steelblue", "white", "darkred")) # 3. Create the heatmap object library(ComplexHeatmap) ht = Heatmap( mat, col = col_fun, cluster_rows = FALSE, cluster_columns = FALSE, show_row_names = FALSE, show_colu...)
• 09:17, 7 August 2025 Brb talk contribs uploaded File:Heatmap-gaps.png (<syntaxhighlight lang='r'> # 1. Prepare the data set.seed(42) mat = matrix(rnorm(30, mean = 0, sd = 1.2), nrow = 5, ncol = 6) mat[2, 1] = -2.5 mat[2, 6] = 2.5 mat[1, 2] = -1.8 mat[4, 4] = 1.8 # 2. Define the color palette library(circlize) col_fun = colorRamp2(c(-2.5, 0, 2.5), c("steelblue", "white", "darkred")) # 3. Create the heatmap object library(ComplexHeatmap) ht = Heatmap( mat, col = col_fun, cluster_rows = FALSE, cluster_columns = FALSE, show_row_names = FALSE, show_colu...)
• 14:18, 29 July 2025 Brb talk contribs created page File:Inkscape-heatmap.svg
• 14:18, 29 July 2025 Brb talk contribs uploaded File:Inkscape-heatmap.svg
• 08:16, 19 July 2025 Brb talk contribs created page File:NemoCaja.png
• 08:16, 19 July 2025 Brb talk contribs uploaded File:NemoCaja.png
• 16:25, 5 July 2025 Brb talk contribs created page File:Cinnamon.png
• 16:25, 5 July 2025 Brb talk contribs uploaded File:Cinnamon.png
• 16:18, 5 July 2025 Brb talk contribs created page File:MATE.png
• 16:18, 5 July 2025 Brb talk contribs uploaded File:MATE.png
• 16:13, 5 July 2025 Brb talk contribs created page File:GNOME.png
• 16:13, 5 July 2025 Brb talk contribs uploaded File:GNOME.png
• 16:06, 5 July 2025 Brb talk contribs created page File:KDE.png
• 16:06, 5 July 2025 Brb talk contribs uploaded File:KDE.png
• 15:52, 5 July 2025 Brb talk contribs created page File:LXDE.png
• 15:52, 5 July 2025 Brb talk contribs uploaded File:LXDE.png
• 15:52, 5 July 2025 Brb talk contribs created page File:Xfce.png
• 15:52, 5 July 2025 Brb talk contribs uploaded File:Xfce.png
• 15:50, 5 July 2025 Brb talk contribs created page File:LXQt.png
• 15:50, 5 July 2025 Brb talk contribs uploaded File:LXQt.png
• 14:16, 2 July 2025 Brb talk contribs created page File:Palbarplot.png
• 14:16, 2 July 2025 Brb talk contribs uploaded File:Palbarplot.png
• 08:07, 13 June 2025 Brb talk contribs created page File:Cauchyos install.png
• 08:07, 13 June 2025 Brb talk contribs uploaded File:Cauchyos install.png
• 12:44, 20 May 2025 Brb talk contribs created page File:Combat DE mod.png (Demonstrate the importance of the 'mod' parameter in sva::ComBat() <syntaxhighlight lang='r'> library(sva) library(limma) library(ggplot2) library(tidyr) set.seed(42) n_genes <- 100 n_samples <- 20 # Group: 10 Case and 10 Control — spread across batches group <- sample(rep(c("Control", "Case"), each=10)) # now randomized batch <- rep(c(1, 2), each=10) # Simulate expression data expr <- matrix(rnorm(n_genes * n_samples, mean=5, sd=1), nrow=n_genes) # Add true signal to 10 genes for Case...)
• 12:44, 20 May 2025 Brb talk contribs uploaded File:Combat DE mod.png (Demonstrate the importance of the 'mod' parameter in sva::ComBat() <syntaxhighlight lang='r'> library(sva) library(limma) library(ggplot2) library(tidyr) set.seed(42) n_genes <- 100 n_samples <- 20 # Group: 10 Case and 10 Control — spread across batches group <- sample(rep(c("Control", "Case"), each=10)) # now randomized batch <- rep(c(1, 2), each=10) # Simulate expression data expr <- matrix(rnorm(n_genes * n_samples, mean=5, sd=1), nrow=n_genes) # Add true signal to 10 genes for Case...)
• 20:47, 17 May 2025 Brb talk contribs created page File:Twoway.png (<syntaxhighlight lang='r'> png("~/Downloads/twoway.png", width=8, height=6, units="in",res=300) par(mar = c(8, 4, 4, 2)) boxplot(y ~ treatment * timepoint, data = df, col = c("skyblue", "lightgreen", "lightpink"), main = "Plant Growth by Treatment and Timepoint", xlab = "", ylab = "Plant Height", xaxt = "n") # Add rotated x-axis labels labels <- levels(interaction(df$treatment, df$timepoint)) axis(1, at = 1:length(labels), labels = FALSE) # Add ticks without labels...)
• 20:47, 17 May 2025 Brb talk contribs uploaded File:Twoway.png (<syntaxhighlight lang='r'> png("~/Downloads/twoway.png", width=8, height=6, units="in",res=300) par(mar = c(8, 4, 4, 2)) boxplot(y ~ treatment * timepoint, data = df, col = c("skyblue", "lightgreen", "lightpink"), main = "Plant Growth by Treatment and Timepoint", xlab = "", ylab = "Plant Height", xaxt = "n") # Add rotated x-axis labels labels <- levels(interaction(df$treatment, df$timepoint)) axis(1, at = 1:length(labels), labels = FALSE) # Add ticks without labels...)