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Figgerin' it out

Jared Andrews j-andrews7

Figgerin' it out
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View sed cheatsheet
# double space a file
sed G
# double space a file which already has blank lines in it. Output file
# should contain no more than one blank line between lines of text.
sed '/^$/d;G'
View gist:f9017de53f2cc6a3c6613a6dfea9aca4
Compiled by Eric Pement - eric [at] version 0.27
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j-andrews7 / BoxScoreScraping.ipynb
Created Feb 24, 2020
A barebones example of basic table parsing for sports data.
View BoxScoreScraping.ipynb
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j-andrews7 / seurat_add_vdj_metadata.R
Last active Nov 1, 2022
A simple function to add 10x V(D)J info to a Seurat object.
View seurat_add_vdj_metadata.R
add_clonotype <- function(tcr_location, seurat_obj){
tcr <- read.csv(paste(tcr_folder,"filtered_contig_annotations.csv", sep=""))
# Remove the -1 at the end of each barcode.
# Subsets so only the first line of each barcode is kept,
# as each entry for given barcode will have same clonotype.
tcr$barcode <- gsub("-1", "", tcr$barcode)
tcr <- tcr[!duplicated(tcr$barcode), ]
# Only keep the barcode and clonotype columns.
View For_Nina_Heatmaps.R
make.heatmaps <- function(dds, res, rld, level, g1, g2, plot_annos=NULL) {
# plot_annos should be a vector of at least two columns from the sample sheet to use for labeling plots.
# g1 and g2 should be strings for the groups to be compared for the level (eg. "Progression", "Response")
# dds must be a DESeqExperiment object.
# rld is the log-transformed dds object.
## Should really make another generic function for the actual heatmap plots and feed it in the pval/lfc values.
# Set color breaks and palatte.
breaks <- c(seq(-3,-1.251,length=250),seq(-1.25,-0.1001,length=250),seq(-0.1,0.1,length=1),seq(0.1001,1.25,length=250),seq(1.251,3,length=250))