markziemann

#!/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 \

markziemann

#!/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 \

markziemann

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]

markziemann

#!/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

markziemann

#!/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

markziemann

#!/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

markziemann

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 %>%