I hereby claim:
- I am lgatto on github.
- I am lgatto (https://keybase.io/lgatto) on keybase.
- I have a public key whose fingerprint is 3228 0F50 8589 B085 9E3D A828 0C03 2B80 46E2 E38A
To claim this, I am signing this object:
## Installation instructions for the R for Mass Spectrometry tutorial | |
## https://rformassspectrometry.github.io/book/ | |
## Install packages | |
if (!requireNamespace("BiocManager", quietly = TRUE)) | |
install.packages("BiocManager") | |
BiocManager::install("tidyverse", ask = FALSE) | |
BiocManager::install("factoextra", ask = FALSE) |
## See https://lgatto.github.io/the-grid-in-r/ | |
plotSquare <- function(x, y, width) { | |
x1 <- x - (width / 2) | |
y1 <- y - (width / 2) | |
x2 <- x1 + width | |
y2 <- y1 + width | |
rect(x1, y1, x2, y2) | |
} |
(defun yank-bibtex-from-doi () | |
"Create and yank bibtex entry from a DOI." | |
(interactive) | |
;; read the doi from minibuffer | |
(setq doi (read-from-minibuffer "doi: ")) | |
;; define the curl shell command | |
(setq cmd | |
(concat | |
"curl -LH \"Accept: application/x-bibtex\" " | |
"https://doi.org/" |
#!/usr/bin/perl | |
## Based on convert.txt by Mike Love | |
## https://gist.github.com/mikelove/5618f935ace6e389d3fbac03224860cd | |
## The script ignores labels and references, un-numbered sections | |
## (section*), quotes and probably a couple of more. It won't deal | |
## with the pre-amble, bibliography and document tags either. Still | |
## useful, though. |
;; grep -h X-Key */*/cur/* | sed -e 's/X-Keywords: //; s/, /\n/g' | sort | uniq > xkeys.txt | |
(setq mu4e-xkeys "~/Maildir/xkeys.txt") | |
(defun read-lines (f) | |
"Return a list of lines of a file at f." | |
(with-temp-buffer | |
(insert-file-contents f) | |
(split-string (buffer-string) "\n" t))) |
;; Pulls and pushes a few github repos from emacs | |
;; Laurent Gatto (https://github.com/lgatto) | |
;; Thanks to Stephen J. Eglen for his help in redirecting to a | |
;; dedicated buffer (https://github.com/sje30) | |
(setq git-dirs '( | |
"~/wd" | |
"~/bin" | |
"~/Documents/org" | |
"~/Documents/roam" |
library(tidyverse) | |
library(scp) | |
## Read the data table | |
x <- read.delim("data/02ng/Task2-SearchTask/AllQuantifiedPeptides.tsv") |> | |
select(-18) |> ## column 18 is all NAs | |
janitor::clean_names() |> | |
rename_with(~ gsub("intensity_ex_auto_", "int_", .x, fixed = TRUE)) |> | |
rename_with(~ gsub("detection_type_ex_auto_", "det_", .x, fixed = TRUE)) |
I hereby claim:
To claim this, I am signing this object:
library(dplyr) | |
library(tibble) | |
library(SummarizedExperiment) | |
library(DEP) | |
library(shiny) | |
library(shinydashboard) | |
ui <- shinyUI( | |
dashboardPage( | |
dashboardHeader(title = "DEP - LFQ"), |
ggPlotMzDelta <- function(delta, aaLabels = TRUE) { | |
stopifnot(require("ggplot2")) | |
## from PSM::getAminoAcids() | |
amino_acids <- | |
structure(list(AA = c("peg", "A", "R", "N", "D", "C", "E", "Q", | |
"G", "H", "I", "L", "K", "M", "F", "P", "S", | |
"T", "W", "Y", "V"), | |
ResidueMass = c(44, 71.03711, 156.10111, 114.04293, | |
115.02694, 103.00919, 129.04259, | |
128.05858, 57.02146, 137.05891, |