https://github.com/milkypostman/melpa
for installing/updating emacs add-on packages
Guangchuang Yu GuangchuangYu
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GuangchuangYu
/ ppurl-alternative.md
Last active
August 29, 2015 14:19
— forked from zjhiphop/ppurl-alternative.md
require(grid)
require(ggplot2)
require(magrittr)
theme_transparent <- function(...) {
theme(panel.background = element_rect(
fill = "transparent",
colour = NA),
plot.background = element_rect(
GuangchuangYu
/ SICP.md
Created
October 23, 2015 06:06
GuangchuangYu
/ hack chipseeker annotation with CpGI
Created
May 2, 2016 14:01
— forked from lpantano/hack chipseeker annotation with CpGI
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| require(TxDb.Hsapiens.UCSC.hg19.knownGene) | |
| txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene | |
| library(ChIPseeker) | |
| library(GenomicRanges) | |
| # Hack chipseeker function to add annotaiton | |
| getGenomicAnnoStat <- function(peakAnno) { | |
| if ( class(peakAnno) == "GRanges" ) | |
| peakAnno <- as.data.frame(peakAnno) | |
| anno <- peakAnno$annotation | |
| ## anno <- sub(" \\(.+", "", anno) |
GuangchuangYu
/ msigdf_clusterprofiler.R
Created
August 17, 2016 17:14
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| ## devtools::install_github("stephenturner/msigdf") | |
| library(msigdf) | |
| library(dplyr) | |
| library(clusterProfiler) | |
| c2 <- msigdf.human %>% | |
| filter(collection == "c2") %>% select(geneset, entrez) %>% as.data.frame | |
| data(geneList) | |
| de <- names(geneList)[1:100] |
GuangchuangYu
/ issues of CorMut.md
Last active
January 4, 2017 07:32
## Access date: 2017-01-04
$ svn log -q |grep 'z.li'
r87229 | z.li | 2014-03-08 12:13:28 +0800 (Sat, 08 Mar 2014)
r85532 | z.li | 2014-01-15 13:00:43 +0800 (Wed, 15 Jan 2014)
r85454 | z.li | 2014-01-12 13:57:16 +0800 (Sun, 12 Jan 2014)
r72578 | z.li | 2013-01-16 15:11:20 +0800 (Wed, 16 Jan 2013)
r72577 | z.li | 2013-01-16 13:43:05 +0800 (Wed, 16 Jan 2013)
GuangchuangYu
/ breast_curve.R
Last active
December 12, 2016 08:55
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| f <- function(a, b) function(y) a * y * log(y, base=10) -1/b * exp(-(b*y - b/exp(1))^4) | |
| y <- seq(0, 1, length.out=100) | |
| cols = colorspace::rainbow_hcl(5) | |
| d1 <- data.frame(x = f(3, 30)(y), y=y, color=cols[1]) | |
| d2 <- data.frame(x = f(2.8, 33)(y), y=y, color=cols[2]) | |
| d3 <- data.frame(x = f(2.5, 36)(y), y=y, color=cols[3]) | |
| d4 <- data.frame(x = f(2.2, 40)(y), y=y, color=cols[4]) | |
| d5 <- data.frame(x = f(2, 50)(y), y=y, color=cols[5]) |
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| qbar <- function(x, verbose=TRUE) { | |
| enc = encoding(quality(x)) | |
| qual <- sapply(seq_along(x), function(i) enc[to_char_vector(x[i])]) | |
| mq <- rowMeans(qual) | |
| if (verbose) { | |
| names(mq) <- NULL | |
| print(mq) | |
| } |
GuangchuangYu
/ worldcup2018.R
Last active
June 21, 2018 03:59
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| d = structure(list(x = c(516.362976074219, 514.883316040039, 510.306549072266, | |
| 502.721382141113, 492.303680419922, 479.293769836426, 463.977825164795, | |
| 446.675720214844, 427.74100112915, 407.568737030029, 386.590072631836, | |
| 365.25927734375, 344.028457641602, 323.352523803711, 303.678215026855, | |
| 285.42236328125, 268.959743499756, 254.630310058594, 242.738302230835, | |
| 233.550735473633, 227.284624099731, 224.07541847229, 223.949848175049, | |
| 226.633100509644, 232.021848678589, 240.107601165771, 248.467231750488, | |
| 256.632625579834, 264.798046112061, 272.827682495117, 279.170124053955, | |
| 284.358814239502, 288.348812103271, 291.169918060303, 292.902908325195, | |
| 293.650428771973, 293.608024597168, 292.990119934082, 291.361457824707, |