Franjo Ivankovic, PhD FranjoIM

🏠

Working from home

Research fellow in psychiatric epidemiology and statistical genetics in @Nealelab at @massgeneralbrigham and @broadinstitute.

FranjoIM / DNAReverseComplement.R

Created April 8, 2020 04:23

DNA Reverse Complement: This function takes a string-type variable containing DNA and it returns its reverse complement

	# Load a library necessary to run this code
	library(stringi)

	# Define the reverse complement function
	rev.comp <- function(DNASeq)
	return(stri_reverse(chartr("acgtACGT", "tgcaTGCA", DNASeq)))

	# Run the code on the dataframe called DF
	DF$Seq <- ifelse (DF$Strand == c("-"), rev.comp(DF$Seq), DF$Seq)
	library(plyr)

FranjoIM / VLOOKUP.R

Created April 8, 2020 04:25

VLOOKUP in R: This function allows to fill one table using the values from another table

	# Load a library necessary to run this code
	library(plyr)

	# Run the code on the dataframes
	CombinedDF <- join(MainDF, LookUpDF, by = "Column")

	head(CombinedDF)

FranjoIM / index.html

Created April 12, 2020 17:44

Progress bars (CSS & HTML)

	<h3> A standalone progress bar </h3>

	<div class="fprogress" >
	<div class="fprogress-bar" id="fA" style="width:90%"> <!-- Edit progress % here -->
	<div class="fbox" id="fA" style="width: 232px"> <!-- Edit shaded area here -->
	<span class="ftext">A Standalone Progress Bar</span>
	</div>
	</div>
	</div>

FranjoIM / GatekeeperBypass.sh

Created July 15, 2020 21:55

Avoid MacOS Gatekeeper check for a specific file

xattr -d com.apple.quarantine file_name

FranjoIM / TSLinkage.csv

Created December 7, 2020 11:00

TS Disorders Linkage Studies

	Chromosomal Location	Summary	Reference

FranjoIM / summary.sh

Created October 14, 2021 19:35

This gist takes a desired file, extracts desired column, and returns a list of unique values with counts.

awk -F ',' '{print $<column_number>}' <file> | sort | uniq -c