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#!/bin/bash | |
# the goal of this script is to determine the fraction of genes in each | |
# biotype class that have annotated functions as determined by membership | |
# in either GO or REACTOME. | |
wget ftp://ftp.ensembl.org/pub/release-100/gtf/homo_sapiens/Homo_sapiens.GRCh38.100.gtf.gz | |
zcat Homo_sapiens.GRCh38.100.gtf.gz \ | |
| grep -w gene \ |
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#!/bin/bash | |
# dependancies: parallel, bedtools, pigz | |
# promoters | |
wget -N ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz | |
GTFZ=Homo_sapiens.GRCh38.98.gtf.gz | |
TSS=tss.bed | |
zcat $GTFZ | grep 'exon_number "1"' | cut -f1,4,5,7,9 \ |
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library(cobs) | |
library(quantreg) | |
library(parallel) | |
library(gplots) | |
interpolate<-function(dat,curve){ | |
interpolate_points<-function(row,dat,curve){ | |
MY_X=dat[row,1] | |
MY_Y=dat[row,2] |
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#!/bin/bash | |
# | |
# author: abu | |
# date: July 3 2019 (ver. 1.1) | |
# description: bash script to install pdftk on Ubuntu 18.04 for amd64 machines | |
############################################################################## | |
# | |
# change to /tmp directory | |
cd /tmp | |
# download packages |
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#!/bin/bash | |
# This script creates a GMT file of genesets classified by protein domains | |
# First need to obtain some data from ensembl biomart | |
# Go to https://www.ensembl.org/biomart/martview/ | |
# Select human database | |
# Select the following attributes: | |
# - Gene stable ID | |
# - Interpro ID | |
# - Interpro Short Description |
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#!/bin/bash | |
echo "Hello world!" | |
formatdb -p F -o T -i Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.cds.all.fa | |
msbar -sequence mysample.fa -count 120 -point 4 -block 0 -codon 0 -outseq mysample_mutated.fa | |
blast2 -m 8 -p blastn -e 0.001 -d Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.cds.all.fa -i mysample_mutated.fa |
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library(stringr) | |
library(text2vec) | |
filelist = list.files(pattern = ".*.txt") | |
x = lapply(filelist, function(x)readLines(x)) | |
prep_fun = function(x) { | |
x %>% | |
# make text lower case | |
str_to_lower %>% |
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