User contributions for Brb
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4 April 2024
- 01:1001:10, 4 April 2024 diff hist +30 ATdeveloper →Release timeline for R/Bioconductor current
3 April 2024
- 17:1617:16, 3 April 2024 diff hist +60 Cancer →Gene expression current
- 16:2116:21, 3 April 2024 diff hist +3,896 Cancer →GI50
- 15:2315:23, 3 April 2024 diff hist +42 ATdeveloper →Release timeline for R/Bioconductor
- 15:2015:20, 3 April 2024 diff hist +341 Genome →RNASeq + ChipSeq
- 14:3714:37, 3 April 2024 diff hist +793 Statistics →Small p-value due to very large sample size
- 13:5313:53, 3 April 2024 diff hist +659 Ggplot2 →Guide functions for finer control
- 12:5812:58, 3 April 2024 diff hist +28 Genome →Immunohistochemistry/IHC
- 12:5612:56, 3 April 2024 diff hist +83 Genome →Integrate RNA-Seq and DNA-Seq
- 12:5312:53, 3 April 2024 diff hist +67 Ggplot2 →Guide functions for finer control
- 12:3812:38, 3 April 2024 diff hist +104 Travel →Videos
- 09:2909:29, 3 April 2024 diff hist +126 Survival data →Logrank test vs Cox model
- 09:0909:09, 3 April 2024 diff hist +71 Office →Find all comments
- 08:3708:37, 3 April 2024 diff hist +157 Office →Find all comments
2 April 2024
- 13:4613:46, 2 April 2024 diff hist +244 VPN →Tailscale
- 13:2613:26, 2 April 2024 diff hist +1,350 VPN →Tailscale
- 01:2901:29, 2 April 2024 diff hist +123 Kodi →TV
29 March 2024
- 23:2923:29, 29 March 2024 diff hist +110 R →Create a factor/categorical variable from a continuous variable: cut() and dplyr::case_when()
- 23:2023:20, 29 March 2024 diff hist +108 Tidyverse →map() and map_dbl()
- 23:1423:14, 29 March 2024 diff hist +120 R →Lexical scoping
- 22:4422:44, 29 March 2024 diff hist +180 Docker Applications →Proxy
- 22:4022:40, 29 March 2024 diff hist +148 Python →Different installation methods
- 22:3622:36, 29 March 2024 diff hist +120 Hardware →HDMI ARC and ext. soundbar
- 22:3422:34, 29 March 2024 diff hist −346 Windows →Burn Windows 7/10 ISO to USB in Ubuntu using WoeUSB
- 22:2522:25, 29 March 2024 diff hist +243 Genome →Quantile normalization
27 March 2024
- 06:3806:38, 27 March 2024 diff hist +86 Shiny →Deploy on Github Pages
- 06:3406:34, 27 March 2024 diff hist +114 R web →webr current
25 March 2024
- 22:2222:22, 25 March 2024 diff hist +514 Rmarkdown →Quarto
- 20:5920:59, 25 March 2024 diff hist −85 Statistics →Akaike information criterion/AIC
21 March 2024
- 22:4122:41, 21 March 2024 diff hist +140 T-test →Check assumptions current
- 22:3722:37, 21 March 2024 diff hist +117 Online tools →Google search
- 22:3522:35, 21 March 2024 diff hist +70 Backup →Pika current
17 March 2024
16 March 2024
- 21:4921:49, 16 March 2024 diff hist +332 Rmarkdown →Dropdown menu
- 16:3916:39, 16 March 2024 diff hist +500 Kodi →Youtube
- 14:3414:34, 16 March 2024 diff hist +58 Docker Applications →Dashy
- 14:3314:33, 16 March 2024 diff hist +64 Docker Applications →Dashy
- 13:3313:33, 16 March 2024 diff hist +139 Health →喝茶 (tea) 的注意事項
- 13:3113:31, 16 March 2024 diff hist +189 Docker Applications →Bioinformatics analyses
- 13:3013:30, 16 March 2024 diff hist +188 Backup →Snapshot
- 11:4511:45, 16 March 2024 diff hist +1,046 Rmarkdown →Download button/embed files
15 March 2024
- 17:2817:28, 15 March 2024 diff hist +159 Rmarkdown →Scrollable code/output
- 16:5416:54, 15 March 2024 diff hist +18 Statistics →Agreement
- 16:1116:11, 15 March 2024 diff hist +197 Venn diagram No edit summary
- 15:4915:49, 15 March 2024 diff hist +84 R →15 Questions All R Users Have About Plots
- 08:2008:20, 15 March 2024 diff hist +101 Rmarkdown →Quarto dashboard
14 March 2024
- 09:3709:37, 14 March 2024 diff hist +138 ICC →Ordinal data
13 March 2024
- 22:2622:26, 13 March 2024 diff hist +221 Rmarkdown →Quarto
- 22:2322:23, 13 March 2024 diff hist +84 Genome →edgeR::filterByExpr
12 March 2024
- 20:2020:20, 12 March 2024 diff hist +168 Genome →Independent Filtering
- 20:1720:17, 12 March 2024 diff hist +528 N File:Filtered R mean.png Use sample mean instead of variance for each gene as the filter statistic. <syntaxhighlight lang='r'> # Follow the previous code chunks M2 <- rowMeans(exprs(ALL_bcrneg)) theta <- seq(0, .80, .01) R_BH <- filtered_R(alpha=.10, M2, p2, theta, method="BH") which.max(R_BH) # 10% <---- so theta=0.1 is the optimal; only 10% genes are removed # 11 max(R_BH) # [1] 270 plot(theta, R_BH, type="l", xlab=expression(theta), ylab="Rejections", main="BH cutoff = 0.1") abline(v=.1, lty=2) <... current
- 17:0717:07, 12 March 2024 diff hist +192 Ggplot2 →Scatterplot with large number of points: alpha
- 13:0813:08, 12 March 2024 diff hist +206 Genome →Independent Filtering
- 11:4111:41, 12 March 2024 diff hist +434 Browser →Privacy-focused browsers
- 11:3811:38, 12 March 2024 diff hist +194 Genome →Ensembl to gene symbol
- 10:4510:45, 12 March 2024 diff hist +97 Javascript →npm install current
- 10:4310:43, 12 March 2024 diff hist +111 Linux →login shell (.bash_profile) vs interactive shell (.bashrc)
- 10:4210:42, 12 March 2024 diff hist +112 NAS →Zimablade
- 10:3910:39, 12 March 2024 diff hist +134 Rstudio →Server
- 10:3510:35, 12 March 2024 diff hist +112 Shiny →Deploy on Github Pages
- 10:2810:28, 12 March 2024 diff hist +142 Self hosting →Network
- 10:2110:21, 12 March 2024 diff hist +705 Raspberry →Share internet
- 10:1110:11, 12 March 2024 diff hist +134 Raspberry →Share internet
- 09:0709:07, 12 March 2024 diff hist +8 Office →Status/presence icons
- 09:0409:04, 12 March 2024 diff hist +777 Ggplot2 →palette()
- 08:5408:54, 12 March 2024 diff hist 0 N File:Rainbow v05.png No edit summary current
- 08:5308:53, 12 March 2024 diff hist 0 N File:Rainbow s05.png No edit summary current
- 08:5208:52, 12 March 2024 diff hist +774 N File:Rainbow default.png <syntaxhighlight lang='r'> library(shiny) # Define the UI ui <- fluidPage( titlePanel("Rainbow Color Palette"), sidebarLayout( sidebarPanel( sliderInput("s_value", "Saturation (s):", min = 0, max = 1, value = 1, step = 0.01), sliderInput("v_value", "Value (v):", min = 0, max = 1, value = 1, step = 0.01) ), mainPanel( plotOutput("rainbow_plot") ) ) ) # Define the server server <- function(input, output) { output$rainbow_plot <- renderPlot({ s <-... current
- 08:2908:29, 12 March 2024 diff hist +412 Genome →Independent Filtering
11 March 2024
- 22:3822:38, 11 March 2024 diff hist −12 Genome →Independent Filtering
- 21:5321:53, 11 March 2024 diff hist +922 Genome →Low read count and filtering
- 21:4121:41, 11 March 2024 diff hist +375 N File:Filtered R.png <syntaxhighlight lang='r'> theta <- seq(0, .80, .01) R_BH <- filtered_R(alpha=.10, S2, p2, theta, method="BH") which.max(R_BH) # 60% <---- so theta=0.6 is the optimal filtering threshold # 61 max(R_BH) # [1] 380 plot(theta, R_BH, type="l", xlab=expression(theta), ylab="Rejections", main="BH cutoff = 0.1") abline(v=.6, lty=2) </syntaxhighlight> current
- 21:3521:35, 11 March 2024 diff hist +3,823 N File:Filtered p.png Note: # x-axis "p cutoff" should be "BH cutoff" or "FDR cutoff". # Each curve represents theta (filtering threshold). For example, theta=.1 means 10% of genes are filtered out before we do multiple testing (or BH adjustment). # It is seen the larger the theta, the more hypotheses are rejected at the same FDR cutoff. For example, #* if theta=0, 251 hypotheses are rejected at FDR=.1 #* if theta=.5, 355 hypotheses are rejected at FDR=.1. <syntaxhighlight lang='r'> BiocManager::install("ALL")... current
- 17:2017:20, 11 March 2024 diff hist +366 Statistics →Correlated data
- 12:3712:37, 11 March 2024 diff hist +555 Genome →Low read count and filtering
- 11:1711:17, 11 March 2024 diff hist +1,447 Genome →DNA methylation, Epigenetics
10 March 2024
- 20:1020:10, 10 March 2024 diff hist +227 Genome →TCGAbiolinks
9 March 2024
- 22:5722:57, 9 March 2024 diff hist +55 NAS →Zimablade
- 22:5322:53, 9 March 2024 diff hist +834 NAS →ODroid xu4
- 19:5719:57, 9 March 2024 diff hist +23 Docker →CasaOS
- 19:5219:52, 9 March 2024 diff hist +137 Docker →CasaOS
8 March 2024
- 16:5416:54, 8 March 2024 diff hist +54 Regression →Example 2: data with outliers
- 16:5116:51, 8 March 2024 diff hist +366 Regression →Example 1: data with outliers
- 16:4916:49, 8 March 2024 diff hist +805 N File:DataOutliers2.png {{Pre}} puree <- read.csv("https://gist.githubusercontent.com/arraytools/e851ed88c7456779557fbf3ed67b157a/raw/9971c61fea1db99acbd9de17ea82679ba9811358/dataOutliers2.csv", header=F) plot(puree[,1], puree[, 2], xlab="X", ylab="Y") abline(lm(V2 ~ V1, data = puree)) # robust regression require(MASS) summary(rlm(V2 ~ V1, data = puree)) abline(rr.huber <- rlm(V2 ~ V1, data = puree), col = "blue") # quantile regression library(quantreg) abline(rq(V2 ~ V1, data=puree, tau = 0.5), col = "red") # theil... current
- 15:1915:19, 8 March 2024 diff hist +155 R packages →Posit Package Manager/RStudio Package Manager
- 12:3912:39, 8 March 2024 diff hist +7 Genome →Low read count and filtering
- 12:1312:13, 8 March 2024 diff hist +1,603 Genome →Low read count and filtering
- 11:1711:17, 8 March 2024 diff hist +1,043 Genome →Low read count and filtering
- 09:1409:14, 8 March 2024 diff hist +95 Online tools →Extract the values of data in a plot
- 08:5908:59, 8 March 2024 diff hist +59 Online tools →Extract the values of data in a plot
- 08:4208:42, 8 March 2024 diff hist +5 Jetson →General information current
- 08:3408:34, 8 March 2024 diff hist +242 Video →Video Trimmer
7 March 2024
- 18:2218:22, 7 March 2024 diff hist +130 Recipes →鍋子噴火
- 18:1818:18, 7 March 2024 diff hist +202 R →factor(x , levels = ...) vs levels(x) <-
- 18:1518:15, 7 March 2024 diff hist +255 R →factor(x , levels = ...) vs levels(x) <-
- 18:0418:04, 7 March 2024 diff hist +198 R →stats::relevel()
- 17:5017:50, 7 March 2024 diff hist +321 Docker Applications →Google photo
- 15:4715:47, 7 March 2024 diff hist +143 Ubuntu →Hardware/Device manager
- 15:4115:41, 7 March 2024 diff hist +122 Reproducible →Share your code and data
- 15:3815:38, 7 March 2024 diff hist +113 KVM →Windows VM current