j-andrews7
/ sed cheatsheet
Created
October 4, 2021 04:02
— forked from ssstonebraker/sed cheatsheet
Sed Cheatsheet
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| FILE SPACING: | |
| # 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 '/^$/d;G' |
j-andrews7
/ gist:f9017de53f2cc6a3c6613a6dfea9aca4
Created
October 4, 2021 03:56
— forked from Rafe/gist:3102414
AWK cheatsheet
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| HANDY ONE-LINE SCRIPTS FOR AWK 30 April 2008 | |
| Compiled by Eric Pement - eric [at] pement.org version 0.27 | |
| Latest version of this file (in English) is usually at: | |
| http://www.pement.org/awk/awk1line.txt | |
| This file will also be available in other languages: | |
| Chinese - http://ximix.org/translation/awk1line_zh-CN.txt | |
| USAGE: |
j-andrews7
/ BoxScoreScraping.ipynb
Created
February 24, 2020 01:48
A barebones example of basic table parsing for sports data.
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j-andrews7
/ seurat_add_vdj_metadata.R
Last active
November 1, 2022 11:16
A simple function to add 10x V(D)J info to a Seurat object.
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| add_clonotype <- function(tcr_location, seurat_obj){ | |
| tcr <- read.csv(paste(tcr_folder,"filtered_contig_annotations.csv", sep="")) | |
| # Remove the -1 at the end of each barcode. | |
| # Subsets so only the first line of each barcode is kept, | |
| # as each entry for given barcode will have same clonotype. | |
| tcr$barcode <- gsub("-1", "", tcr$barcode) | |
| tcr <- tcr[!duplicated(tcr$barcode), ] | |
| # Only keep the barcode and clonotype columns. |
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| 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)) |