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Combined display of all available logs of 太極. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).
- 17:26, 19 October 2022 Brb talk contribs created page File:NC better kNN.png (The green color is a new observation (Sensitive). By using the kNN method, it will be assigned to Resistant b/c it is closer to the Resistant group. However, using the NC, the distance of it to the Resistant group centroid is 8.42 which is larger than the distance of it to the Sensitive groups centroid 7.31. So NC classified it to Sensitive. Color annotation: green=LOO obs, black=centroid in each class.)
- 17:26, 19 October 2022 Brb talk contribs uploaded File:NC better kNN.png (The green color is a new observation (Sensitive). By using the kNN method, it will be assigned to Resistant b/c it is closer to the Resistant group. However, using the NC, the distance of it to the Resistant group centroid is 8.42 which is larger than the distance of it to the Sensitive groups centroid 7.31. So NC classified it to Sensitive. Color annotation: green=LOO obs, black=centroid in each class.)
- 11:03, 12 October 2022 Brb talk contribs created page File:Foldchangefilter.png (<pre> LFC <- log2(1.5) x <- c(0, 0, 0, 0, 0, 0, 0, 0, 3.22, 0, 0, 0, 8.09, 0, 0.65, 0, 0, 0, 0, 0, 3.38, 0, 5.63, 7.46, 0, 0, 4.38, 0) plot(x, y = 1:28, xlab="log2 intensity", ylab="samples") abline(v=LFC, lty="dashed") axis(side=3,at=LFC, labels="LFC", tick=FALSE, line=0) </pre>)
- 11:03, 12 October 2022 Brb talk contribs uploaded File:Foldchangefilter.png (<pre> LFC <- log2(1.5) x <- c(0, 0, 0, 0, 0, 0, 0, 0, 3.22, 0, 0, 0, 8.09, 0, 0.65, 0, 0, 0, 0, 0, 3.38, 0, 5.63, 7.46, 0, 0, 4.38, 0) plot(x, y = 1:28, xlab="log2 intensity", ylab="samples") abline(v=LFC, lty="dashed") axis(side=3,at=LFC, labels="LFC", tick=FALSE, line=0) </pre>)
- 16:39, 11 October 2022 Brb talk contribs created page File:Cvglmnetplot.png (<pre> n <- 100 set.seed(1) x1 <- rnorm(n) e <- rnorm(n)*.01 y <- x1 + e x4 <- x fit <- cv.glmnet(x=cbind(x1, x4, matrix(rnorm(n*10), nr=n)), y=y) plot (fit) </pre>)
- 16:39, 11 October 2022 Brb talk contribs uploaded File:Cvglmnetplot.png (<pre> n <- 100 set.seed(1) x1 <- rnorm(n) e <- rnorm(n)*.01 y <- x1 + e x4 <- x fit <- cv.glmnet(x=cbind(x1, x4, matrix(rnorm(n*10), nr=n)), y=y) plot (fit) </pre>)
- 07:57, 7 October 2022 Brb talk contribs created page Prediction (Created page with "= Gradient boost = * https://en.wikipedia.org/wiki/Gradient_boosting * [https://datascienceplus.com/gradient-boosting-in-r/ Gradient boosting in R] == GBDT: Gradient Boosting...")
- 14:12, 6 October 2022 Brb talk contribs created page File:Greedypairs.png
- 14:12, 6 October 2022 Brb talk contribs uploaded File:Greedypairs.png
- 11:11, 6 October 2022 Brb talk contribs uploaded a new version of File:Barplot base.png
- 11:06, 6 October 2022 Brb talk contribs created page File:Barplot ggplot2.png
- 11:06, 6 October 2022 Brb talk contribs uploaded File:Barplot ggplot2.png
- 11:06, 6 October 2022 Brb talk contribs created page File:Barplot base.png
- 11:06, 6 October 2022 Brb talk contribs uploaded File:Barplot base.png
- 11:50, 30 August 2022 Brb talk contribs created page File:Geomcolviridis.png (Modify the example from https://datavizpyr.com/re-ordering-bars-in-barplot-in-r/ to allow filled colors and facet. <pre> library(tidyverse) library(gapminder) library(viridis) theme_set(theme_bw(base_size=16)) pop_df <- gapminder %>% filter(year==2007)%>% group_by(continent) %>% summarize(pop_in_millions=sum(pop)/1e06) pop_df2 <- tibble(class=rbinom(nrow(pop_df), 1, .5), pop_df) pop_df2 <- pop_df2 |> mutate(pop_in_millions = pop_in_millions-1900) pop_df2 %>% ggplot(aes...)
- 11:50, 30 August 2022 Brb talk contribs uploaded File:Geomcolviridis.png (Modify the example from https://datavizpyr.com/re-ordering-bars-in-barplot-in-r/ to allow filled colors and facet. <pre> library(tidyverse) library(gapminder) library(viridis) theme_set(theme_bw(base_size=16)) pop_df <- gapminder %>% filter(year==2007)%>% group_by(continent) %>% summarize(pop_in_millions=sum(pop)/1e06) pop_df2 <- tibble(class=rbinom(nrow(pop_df), 1, .5), pop_df) pop_df2 <- pop_df2 |> mutate(pop_in_millions = pop_in_millions-1900) pop_df2 %>% ggplot(aes...)
- 10:31, 30 August 2022 Brb talk contribs created page File:ViridisDefault.png (<pre> library(viridis) n = 200 image( 1:n, 1, as.matrix(1:n), col = viridis(n, option = "D"), xlab = "viridis n", ylab = "", xaxt = "n", yaxt = "n", bty = "n" ) </pre>)
- 10:31, 30 August 2022 Brb talk contribs uploaded File:ViridisDefault.png (<pre> library(viridis) n = 200 image( 1:n, 1, as.matrix(1:n), col = viridis(n, option = "D"), xlab = "viridis n", ylab = "", xaxt = "n", yaxt = "n", bty = "n" ) </pre>)
- 10:08, 30 August 2022 Brb talk contribs created page File:ScaleFillViridisDiscrete.png (See https://r-graph-gallery.com/79-levelplot-with-ggplot2.html <pre> library(ggplot2) # library(hrbrthemes) # Dummy data x <- LETTERS[1:20] y <- paste0("var", seq(1,20)) data <- expand.grid(X=x, Y=y) data$Z <- runif(400, 0, 5) library(viridis) ggplot(data, aes(X, Y, fill= Z)) + geom_tile() + scale_fill_viridis(discrete=FALSE) </pre>)
- 10:08, 30 August 2022 Brb talk contribs uploaded File:ScaleFillViridisDiscrete.png (See https://r-graph-gallery.com/79-levelplot-with-ggplot2.html <pre> library(ggplot2) # library(hrbrthemes) # Dummy data x <- LETTERS[1:20] y <- paste0("var", seq(1,20)) data <- expand.grid(X=x, Y=y) data$Z <- runif(400, 0, 5) library(viridis) ggplot(data, aes(X, Y, fill= Z)) + geom_tile() + scale_fill_viridis(discrete=FALSE) </pre>)
- 14:19, 29 August 2022 Brb talk contribs created page File:Rbiomirgs barall.png
- 14:19, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs barall.png
- 14:17, 29 August 2022 Brb talk contribs created page File:Rbiomirgs bar.png
- 14:17, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs bar.png
- 14:17, 29 August 2022 Brb talk contribs created page File:Rbiomirgs volcano.png
- 14:17, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs volcano.png
- 07:08, 27 August 2022 Brb talk contribs created page File:FgseaPlotTop.png
- 07:08, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotTop.png
- 06:34, 27 August 2022 Brb talk contribs created page File:FgseaPlotSmall2.png
- 06:34, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotSmall2.png
- 06:34, 27 August 2022 Brb talk contribs created page File:FgseaPlotSmall.png
- 06:34, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotSmall.png
- 06:33, 27 August 2022 Brb talk contribs created page File:FgseaPlot.png
- 06:33, 27 August 2022 Brb talk contribs uploaded File:FgseaPlot.png
- 15:02, 23 August 2022 Brb talk contribs created page File:ComplexHeatmap1.png (<pre> library(ComplexHeatmap) set.seed(123) ng <- 10; n <- 10 mat = matrix(rnorm(ng * n), n) rownames(mat) = paste0("R", 1:ng) colnames(mat) = paste0("C", 1:n) bin <- sample(c("resistant", "sensitive"), n, replace = TRUE) tgi <- runif(n) # sort the columns by tgi ord <- order(tgi) col_fun = circlize::colorRamp2(range(tgi), c("#DEEBF7", "#084594")) column_ha = HeatmapAnnotation(tgi = tgi[ord], bin = bin[ord], col = list(tgi = col_fun,...)
- 15:02, 23 August 2022 Brb talk contribs uploaded File:ComplexHeatmap1.png (<pre> library(ComplexHeatmap) set.seed(123) ng <- 10; n <- 10 mat = matrix(rnorm(ng * n), n) rownames(mat) = paste0("R", 1:ng) colnames(mat) = paste0("C", 1:n) bin <- sample(c("resistant", "sensitive"), n, replace = TRUE) tgi <- runif(n) # sort the columns by tgi ord <- order(tgi) col_fun = circlize::colorRamp2(range(tgi), c("#DEEBF7", "#084594")) column_ha = HeatmapAnnotation(tgi = tgi[ord], bin = bin[ord], col = list(tgi = col_fun,...)
- 14:19, 22 August 2022 Brb talk contribs created page File:Doubledip.png (<pre> ng <- 1000 # number of genes ns <- 100 # number of samples k <- 2 # number of groups alpha <- .001 # cutoff of selecting sig genes set.seed(1) x = matrix(rnorm(ng * ns), nr= ns) # samples x features hc = hclust(dist(x)) plot(hc) grp = cutree(hc, k=k) # vector of group membership ex <- t(x) r1 <- genefilter::rowttests(ex, factor(grp)) sum(r1$p.value < alpha) # 2 hist(r1$p.value) i <- which(r1$p.value < alpha) i1 <- i[1] ; i2 <- i[2] plot(x[, i1], x[, i2], col = grp, pch= 16, cex=1...)
- 14:19, 22 August 2022 Brb talk contribs uploaded File:Doubledip.png (<pre> ng <- 1000 # number of genes ns <- 100 # number of samples k <- 2 # number of groups alpha <- .001 # cutoff of selecting sig genes set.seed(1) x = matrix(rnorm(ng * ns), nr= ns) # samples x features hc = hclust(dist(x)) plot(hc) grp = cutree(hc, k=k) # vector of group membership ex <- t(x) r1 <- genefilter::rowttests(ex, factor(grp)) sum(r1$p.value < alpha) # 2 hist(r1$p.value) i <- which(r1$p.value < alpha) i1 <- i[1] ; i2 <- i[2] plot(x[, i1], x[, i2], col = grp, pch= 16, cex=1...)
- 10:21, 10 August 2022 Brb talk contribs created page File:Ruspini.png (library(cluster) # ruspini is 75 x 2 data(ruspini) hc <- hclust(dist(ruspini), "ave"); plot(hc) # si <- silhouette(groups, dist(ruspini)) # plot(si, main = paste("k = ", 4)) op <- par(mfrow= c(3,2), oma= c(0,0, 3, 0), mgp= c(1.6,.8,0), mar= .1+c(4,2,2,2)) plot(hc) for(k in 2:6) { groups<- cutree(hc, k=k) si <- silhouette(groups, dist(ruspini)) plot(si, main = paste("k = ", k)) } par(op))
- 10:21, 10 August 2022 Brb talk contribs uploaded File:Ruspini.png (library(cluster) # ruspini is 75 x 2 data(ruspini) hc <- hclust(dist(ruspini), "ave"); plot(hc) # si <- silhouette(groups, dist(ruspini)) # plot(si, main = paste("k = ", 4)) op <- par(mfrow= c(3,2), oma= c(0,0, 3, 0), mgp= c(1.6,.8,0), mar= .1+c(4,2,2,2)) plot(hc) for(k in 2:6) { groups<- cutree(hc, k=k) si <- silhouette(groups, dist(ruspini)) plot(si, main = paste("k = ", k)) } par(op))
- 19:55, 23 June 2022 Brb talk contribs created page File:Tidyheatmap.png
- 19:55, 23 June 2022 Brb talk contribs uploaded File:Tidyheatmap.png
- 15:22, 21 June 2022 Brb talk contribs created page File:BatchqcPCA.png
- 15:22, 21 June 2022 Brb talk contribs uploaded File:BatchqcPCA.png
- 15:22, 21 June 2022 Brb talk contribs created page File:BatchqcDE.png
- 15:22, 21 June 2022 Brb talk contribs uploaded File:BatchqcDE.png
- 15:21, 21 June 2022 Brb talk contribs created page File:BatchqcVariation.png
- 15:21, 21 June 2022 Brb talk contribs uploaded File:BatchqcVariation.png
- 15:20, 21 June 2022 Brb talk contribs created page File:BatchqcSummary.png
- 15:20, 21 June 2022 Brb talk contribs uploaded File:BatchqcSummary.png
- 20:43, 8 June 2022 Brb talk contribs created page Fstab (Created page with "* man fstab * https://help.ubuntu.com/community/Fstab ** Format: [Device] [Mount Point] [File System Type] [Options] [Dump] [Pass] ** <dump> Enable or disable backing up of th...")
- 18:02, 4 June 2022 Brb talk contribs created page File:Heatmap rdylbu.png
- 18:02, 4 June 2022 Brb talk contribs uploaded File:Heatmap rdylbu.png
- 15:02, 4 June 2022 Brb talk contribs created page Self hosting (Created page with "= Resource = * [https://github.com/mycroftwilde/portainer_templates Helpful Youtube Channels for Self-Hosting] = [http://www.proxmox.com/en/ Proxmox Virtual Environment] = *...")
- 10:06, 27 May 2022 Brb talk contribs created page File:Inter gg2.png
- 10:06, 27 May 2022 Brb talk contribs uploaded File:Inter gg2.png
- 09:51, 27 May 2022 Brb talk contribs created page File:Inter gg.png
- 09:51, 27 May 2022 Brb talk contribs uploaded File:Inter gg.png
- 09:51, 27 May 2022 Brb talk contribs created page File:Inter base.png
- 09:51, 27 May 2022 Brb talk contribs uploaded File:Inter base.png
- 09:16, 27 May 2022 Brb talk contribs uploaded a new version of File:Inter base.svg
- 09:04, 27 May 2022 Brb talk contribs created page File:Inter base.svg
- 09:04, 27 May 2022 Brb talk contribs uploaded File:Inter base.svg
- 10:08, 26 May 2022 Brb talk contribs created page File:LogisticFail.svg (> set.seed(1234); n <- 16; mu=3; x <- c(rnorm(n), rnorm(n, mu)); y <- rep(0:1, each=n) > summary(glm(y ~ x, family = binomial)); plot(x, y))
- 10:08, 26 May 2022 Brb talk contribs uploaded File:LogisticFail.svg (> set.seed(1234); n <- 16; mu=3; x <- c(rnorm(n), rnorm(n, mu)); y <- rep(0:1, each=n) > summary(glm(y ~ x, family = binomial)); plot(x, y))
- 13:35, 16 May 2022 Brb talk contribs created page Batch effect (Created page with "= Merging two gene expression studies, ComBat = * [https://www.coursera.org/lecture/statistical-genomics/module-2-overview-1-12-cbqYZ Statistics for Genomic Data Science] (Cou...")
- 12:56, 10 May 2022 Brb talk contribs created page File:ColorRampBlueRed.png
- 12:56, 10 May 2022 Brb talk contribs uploaded File:ColorRampBlueRed.png
- 09:34, 30 April 2022 Brb talk contribs created page Docker Applications (Created page with "[https://kuonsam.miraheze.org/wiki/Setting_Up_a_Docker_Server#Install_Docker-compose Setting Up a Docker Server] (host OS is CentOS) = Dockerizing Compiled Software = https:/...")
- 19:39, 24 March 2022 Brb talk contribs created page File:Rerrorbars.png (<pre> library(ggplot2) df <- ToothGrowth df$dosef <- as.factor(df$dose) library(dplyr) df.summary <- df %>% group_by(dosef) %>% summarise( sd = sd(len, na.rm = TRUE), len = mean(len) ) df.summary p1 <- ggplot(df, aes(dosef, len)) + geom_jitter(position = position_jitter(0.2, seed=1), color = "darkgray") + geom_point(aes(x=dosef, y=len), shape="+", size=8, data=df.summary) + geom_errorbar(aes(ymin = len-sd, ymax = len+sd), width=.2, data = df.summary) df.summary$dose <...)
- 19:39, 24 March 2022 Brb talk contribs uploaded File:Rerrorbars.png (<pre> library(ggplot2) df <- ToothGrowth df$dosef <- as.factor(df$dose) library(dplyr) df.summary <- df %>% group_by(dosef) %>% summarise( sd = sd(len, na.rm = TRUE), len = mean(len) ) df.summary p1 <- ggplot(df, aes(dosef, len)) + geom_jitter(position = position_jitter(0.2, seed=1), color = "darkgray") + geom_point(aes(x=dosef, y=len), shape="+", size=8, data=df.summary) + geom_errorbar(aes(ymin = len-sd, ymax = len+sd), width=.2, data = df.summary) df.summary$dose <...)
- 19:37, 24 March 2022 Brb talk contribs created page File:Rerrorbar.svg (<pre> library(ggplot2) df <- ToothGrowth df$dosef <- as.factor(df$dose) library(dplyr) df.summary <- df %>% group_by(dosef) %>% summarise( sd = sd(len, na.rm = TRUE), len = mean(len) ) df.summary p1 <- ggplot(df, aes(dosef, len)) + geom_jitter(position = position_jitter(0.2, seed=1), color = "darkgray") + geom_point(aes(x=dosef, y=len), shape="+", size=8, data=df.summary) + geom_errorbar(aes(ymin = len-sd, ymax = len+sd), width=.2, data = df.summary) df.summary$dose <...)
- 19:37, 24 March 2022 Brb talk contribs uploaded File:Rerrorbar.svg (<pre> library(ggplot2) df <- ToothGrowth df$dosef <- as.factor(df$dose) library(dplyr) df.summary <- df %>% group_by(dosef) %>% summarise( sd = sd(len, na.rm = TRUE), len = mean(len) ) df.summary p1 <- ggplot(df, aes(dosef, len)) + geom_jitter(position = position_jitter(0.2, seed=1), color = "darkgray") + geom_point(aes(x=dosef, y=len), shape="+", size=8, data=df.summary) + geom_errorbar(aes(ymin = len-sd, ymax = len+sd), width=.2, data = df.summary) df.summary$dose <...)
- 14:13, 18 March 2022 Brb talk contribs created page File:SnrVScor.png
- 14:13, 18 March 2022 Brb talk contribs uploaded File:SnrVScor.png
- 14:10, 18 March 2022 Brb talk contribs created page File:CorVSsnr.svg
- 14:10, 18 March 2022 Brb talk contribs uploaded File:CorVSsnr.svg
- 19:22, 14 March 2022 Brb talk contribs created page Filesystem (Created page with "= squashfs = '''squashfs''' is a heavy-compression based read-only filesystem that is capable of compressing 2 to 3 GB of data onto a 700MB. Linux liveCD are built using squas...")
- 14:15, 5 March 2022 Brb talk contribs created page File:AntiX21 mmedia.png
- 14:15, 5 March 2022 Brb talk contribs uploaded File:AntiX21 mmedia.png
- 15:12, 9 February 2022 Brb talk contribs created page Cancer (Created page with "= 癌症 Cancer = * [https://1drv.ms/u/s!Am92ICmSSQXujWZnlGy0JJjK1Gj6 生活中9種引發癌症最危險的因子] * [https://health.udn.com/health/story/6008/3053686 用手...")
- 22:31, 2 February 2022 Brb talk contribs created page File:WewatchJetsonnano-min.png
- 22:31, 2 February 2022 Brb talk contribs uploaded File:WewatchJetsonnano-min.png
- 10:17, 29 January 2022 Brb talk contribs created page Regression (Created page with "= Linear Regression = * [https://leanpub.com/regmods Regression Models for Data Science in R] by Brian Caffo * [https://avehtari.github.io/ROS-Examples/ Regression and Other S...")
- 15:13, 29 December 2021 Brb talk contribs created page Eink (Created page with "* https://twitter.com/hashtag/epaper * https://github.com/topics/eink * [https://www.raspberrypi.org/blog/using-e-ink-raspberry-pi/ Using E Ink displays with a Raspberry Pi] *...")
- 10:33, 19 December 2021 Brb talk contribs created page Tidymodels (Created page with "= Tidymodels and tune = * [https://cran.r-project.org/web/packages/tidymodels/index.html tidymodels], [https://cran.r-project.org/web/packages/tune/index.html tune] * https://...")
- 14:28, 14 December 2021 Brb talk contribs created page Venn diagram (Created page with "* [https://cran.r-project.org/web/packages/eulerr/index.html eulerr] package * [https://codingenes.wordpress.com/2013/09/30/visualization-biological-data-using-proportional-ve...")
- 11:12, 27 November 2021 Brb talk contribs created page Remote desktop (Created page with "= x11vnc = * [https://www.makeuseof.com/install-ubuntu-vnc-server-linux/ How to Install and Run a VNC Server on Ubuntu Linux] 2021 [https://www.cloudsavvyit.com/7725/how-to-co...")
- 10:45, 27 November 2021 Brb talk contribs created page Chroot (Created page with "* https://help.ubuntu.com/community/BasicChroot * https://help.ubuntu.com/community/DebootstrapChroot * http://www.thegeekstuff.com/2010/01/debootstrap-minimal-debian-ubuntu-i...")
- 10:11, 17 November 2021 Brb talk contribs created page File:Atnormalize.png
- 10:11, 17 November 2021 Brb talk contribs uploaded File:Atnormalize.png
- 09:41, 22 October 2021 Brb talk contribs created page Jetson (Created page with "Jetson nano https://www.nvidia.com/en-us/autonomous-machines/embedded-systems/jetson-nano/ * [https://youtu.be/4cftyAq_J9g Now One Of The BEST SBCs For Emulation Project ARES...")
- 10:31, 11 October 2021 Brb talk contribs created page Linux Distribution (Created page with "== Run from RAM == [https://en.wikipedia.org/wiki/List_of_Linux_distributions_that_run_from_RAM List of Linux distributions that run from RAM] == Linux Distro for Your Cloud...")
- 12:22, 15 September 2021 Brb talk contribs created page File:Jupyter.drawio.png
- 12:22, 15 September 2021 Brb talk contribs uploaded File:Jupyter.drawio.png
- 09:43, 14 August 2021 Brb talk contribs created page File:VscodeR.png
- 09:43, 14 August 2021 Brb talk contribs uploaded File:VscodeR.png
- 14:42, 12 August 2021 Brb talk contribs created page Bootstrap (Created page with "= General = * [https://en.wikipedia.org/wiki/Bootstrapping_%28statistics%29 Bootstrap] from Wikipedia. ** This contains an overview of different methods for computing bootstr...")
- 14:00, 11 August 2021 Brb talk contribs created page Pharmacokinetics (Created page with "* https://en.wikipedia.org/wiki/Pharmacodynamics, https://en.wikipedia.org/wiki/Pharmacokinetics * [https://www.acnp.org/g4/GN401000085/CH084.html Pharmacokinetics and Pharmac...")
- 11:31, 31 July 2021 Brb talk contribs created page Alpine (Created page with "* [https://alpinelinux.org/ Alpine Linux] * https://en.wikipedia.org/wiki/Alpine_Linux * [https://www.makeuseof.com/alpine-linux-explained/ Alpine Linux: A Breath of Fresh Mou...")