Miguel D Prieto G azmigueldario

M.D., MSc. Research interests include public health, infectious diseases and molecular epidemiology

aofarrel / Get metadata for NCBI BioSamples.py

Created May 10, 2024 19:27

	# Notes:
	# * Works for SAMN, SAME, and SAMD BioSamples (should also work for SRS/ERS format)
	# * Grabs date and location of sample isolation, host, sample source, and strain
	# * edirect tools needs to be on $PATH, or you can use my Docker image for a pre-installed version: https://hub.docker.com/r/ashedpotatoes/sranwrp/tags
	# * elink is known to randomly fail so this code doesn't use it -- however, without elink, you can't get the SRA reads (SRR/ERR/DRR) that make up a BioSample


	import subprocess

	biosamples = ["SAMEA6451356","SAMEA6451357","SAMEA6451358","SAMEA6451360","SAMEA6451361","SAMEA6451362","SAMEA6451363","SAMEA6451366","SAMEA6451367","SAMEA6451368","SAMEA6451369","SAMEA6451370","SAMEA6451371","SAMEA6451372","SAMEA6451373","SAMEA6451374","SAMEA6451375","SAMEA6451377"]

timedreamer / GO_anlaysis_using_topGO.R

Created December 14, 2022 19:56

Use topGO package for GO analysis in R.

	# 0. Prep -----------------------------------------------------------------

	library(tidyverse)
	library(here)

	# 1. Load and clean EggNOG output -----------------------------------------

	## The output was downloaded from the eggnog-mapper online run.
	eggnog_go <- read_tsv(here("data", "misc", "out.emapper.annotations.gz"),
	skip = 4) %>%

ag1805x / GRCh38.rRNA.interval_list

Created July 24, 2019 11:06

	#!/usr/bin/env bash
	# make_rRNA.sh
	# Kamil Slowikowski
	# December 12, 2014
	#
	# Modified: Arindam Ghosh (July 24, 2019 )
	#
	#
	# Referenc Genome: GRCh38.p5 Ensembl release 84
	#

lukehedger / ffmpeg-compress-mp4

Last active September 18, 2024 18:02

Compress mp4 using FFMPEG

$ ffmpeg -i input.mp4 -vcodec h264 -acodec mp2 output.mp4

Verrus / outfmt6_m8_NCBI_Blastheader.txt

Last active December 6, 2023 10:02

NCBI Blast output header -outfmt 6 or -m8 header in tabular form

query_id        subject_id      pct_identity    aln_length      n_of_mismatches gap_openings    q_start q_end   s_start   s_end   e_value bit_score