User contributions for Brb
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12 January 2023
- 16:4416:44, 12 January 2023 diff hist +166 Genome →Tumor mutational burden
- 16:3616:36, 12 January 2023 diff hist +493 Genome →Tumor mutational burden
- 12:3612:36, 12 January 2023 diff hist +67 GSEA →Examples
- 12:2112:21, 12 January 2023 diff hist +208 GSEA →Examples
- 12:1812:18, 12 January 2023 diff hist +747 N File:GseaTable2.png An example of a plot from 10 non-enriched pathways. <pre> data(examplePathways) data(exampleRanks) fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000, minSize=15, maxSize=100) fgseaRes[order(pval, decreasing = T),][1:10, c('NES', 'pval')] # NES pval # 1: -0.4050950 1.0000000 # 2: -0.4050950 1.0000000 # 3: -0.4966664 0.9932584 # 4: 0.4804114 0.9870610 # 5: 0.4804114 0.9870610 # 6: 0.4804114 0.9870610 # 7: 0.4804114 0.9870610 # 8: 0.4955139 0.9854... current
- 12:0112:01, 12 January 2023 diff hist +1,315 N File:GseaTable.png <pre> data(examplePathways) data(exampleRanks) fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000, minSize=15, maxSize=100) # I pick 5 pathways with + NES and 5 pathways with - NES. fgseaRes[order(pval), ][62:71, c('pathway', 'NES')] # pathway NES # 1: 5992282_ECM_proteoglycans 1.984081 # 2: 5992219_Regulation_of_cholesterol_biosynthesis_by_SREBP_SREBF_ 1.95... current
- 10:5510:55, 12 January 2023 diff hist +158 GSEA →Examples
11 January 2023
- 18:1718:17, 11 January 2023 diff hist +82 Statistics →Mixed Effect Model
- 18:0918:09, 11 January 2023 diff hist +51 Genome →Shrinkage estimators
- 18:0218:02, 11 January 2023 diff hist +1,314 Genome →Undifferentiated cancer
- 17:5617:56, 11 January 2023 diff hist +6,094 Genome →Shrinkage estimators
- 16:0416:04, 11 January 2023 diff hist +8 Genome →Shrinkage estimators
- 16:0316:03, 11 January 2023 diff hist +1,754 Genome →Shrinkage estimators
- 15:4115:41, 11 January 2023 diff hist +1,019 Genome →Shrinkage estimators
- 09:0709:07, 11 January 2023 diff hist +364 Grub →Dual boot
10 January 2023
- 21:1121:11, 10 January 2023 diff hist +55 R →Organize R research project
- 20:5620:56, 10 January 2023 diff hist +131 R packages →install a package as it existed on a specific date/snapshot: mran repository
- 20:5120:51, 10 January 2023 diff hist +76 Virtualbox →Virtual networks
- 16:4916:49, 10 January 2023 diff hist −3,123 Regression →Confounders, confounding
- 16:4816:48, 10 January 2023 diff hist +5,080 T-test →Two-way ANOVA
- 16:2416:24, 10 January 2023 diff hist +3,188 Regression →Confounders, confounding
- 16:0416:04, 10 January 2023 diff hist +1,532 Life →Best way to persuade someone that they're wrong
- 14:2114:21, 10 January 2023 diff hist +247 Genome →Base quality, Mapping quality, Variant quality
9 January 2023
- 21:2921:29, 9 January 2023 diff hist +58 Heatmap →Reorder dendrograms
- 16:1716:17, 9 January 2023 diff hist +175 Chrome →Reduce memory/manage tabs
8 January 2023
- 19:3619:36, 8 January 2023 diff hist +163 AI →ChatGPT
- 19:3419:34, 8 January 2023 diff hist +167 Windows →Local accounts
- 19:3319:33, 8 January 2023 diff hist +158 Docker Applications →Run a benchmark program on ARM devices
- 19:3119:31, 8 January 2023 diff hist +9 Life →Pension, Federal Employees Retirement System/FERS
- 19:3019:30, 8 January 2023 diff hist +66 Life No edit summary
- 19:2619:26, 8 January 2023 diff hist +92 AI →ChatGPT
- 19:2519:25, 8 January 2023 diff hist +101 Recipes →飯糰 (Onigiri, rice ball), 韓國烤肉
- 19:2319:23, 8 January 2023 diff hist +178 Windows →How to Secure Your Accounts With 2FA
- 19:2119:21, 8 January 2023 diff hist +160 Windows →Windows 11
- 19:2019:20, 8 January 2023 diff hist +220 R →plyr and dplyr packages
- 19:1719:17, 8 January 2023 diff hist +164 Genome →Integrate/combine Omics
- 16:4716:47, 8 January 2023 diff hist +31 Heatmap →Reorder dendrograms
- 16:4116:41, 8 January 2023 diff hist +1,100 Heatmap →Reorder dendrograms
- 15:5715:57, 8 January 2023 diff hist 0 Heatmap →Rowv, Colv: reorder of rows and columns
- 13:4813:48, 8 January 2023 diff hist +27 Heatmap →Rowv, Colv: reorder of rows and columns
- 12:2412:24, 8 January 2023 diff hist +335 Heatmap →Rowv, Colv: reorder of rows and columns
- 12:1512:15, 8 January 2023 diff hist +788 Heatmap →Rowv, Colv: reorder of rows and columns
- 12:1512:15, 8 January 2023 diff hist +321 N File:Reorder.dendrogram.png <pre> set.seed(123) x <- rnorm(20) hc <- hclust(dist(x)) dd <- as.dendrogram(hc) par(mfrow=c(3, 1)) plot(dd, main = "random dendrogram 'dd'") # not the same as reorder(dd, 1:20) plot(reorder(dd, 20:1), main = 'reorder(dd, 20:1, sum)') plot(reorder(dd, 20:1, mean), main = 'reorder(dd, 20:1, mean)') </pre> current
- 11:1111:11, 8 January 2023 diff hist +2,127 Heatmap No edit summary
- 10:1610:16, 8 January 2023 diff hist +164 Chrome →Adblock for Youtube
- 00:1200:12, 8 January 2023 diff hist +417 Heatmap →Reorder dendrograms
7 January 2023
- 21:3821:38, 7 January 2023 diff hist +387 Heatmap →Heatmap split
- 21:3721:37, 7 January 2023 diff hist +1,121 N File:ComplexHeatmap2.png <syntaxhighlight lang="rsplus"> # Simulate data library(ComplexHeatmap) ng <- 30; ns <- 20 set.seed(1) mat <- matrix(rnorm(ng*ns), nr=ng, nc=ns) colnames(mat) <- 1:ns rownames(mat) <- 1:ng # color bar on RHS ind_e <- 1:round(ng/3) ind_m <- (1+round(ng/3)):ng epimes <- rep(c("epi", "mes"), c(length(ind_e), length(ind_m))) row_ha <- rowAnnotation(epimes = epimes, col = list(epimes = c("epi" = "orange", "mes" = "darkgreen"))) # color bar on Top tumortype <- rep(c("carcinoma", "sarcoma"... current
- 15:5115:51, 7 January 2023 diff hist +168 Heatmap →Heatmap split
- 15:2015:20, 7 January 2023 diff hist +212 Genome →Z-score transformation