mfcovington

cell culture
purification

mfcovington

function extract_sequences {
    GENE=$1
    EXON=$2

    CHR=$3

    BAM_START=$4
    BAM_END=$5

    EXON_START=$6

mfcovington

sudo yum -y update
sudo yum install -y gcc48-plugin-devel.x86_64

sudo mkdir /installs
cd /installs

sudo wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
sudo tar -xjf samtools-1.3.1.tar.bz2
cd samtools-1.3.1

mfcovington

library(edgeR)
library(ggplot2)

setwd('/path/to/counts-directory')

counts.files <- list.files(pattern="\\.counts$")
sample.names <- c('H6 GFP #1', 'H6 GFP #2', 'HIF-2α #3', 'HIF-2α #4', 'HIF-1α #7', 'HIF-1α #8')
counts.df <- readDGE(counts.files, labels=sample.names, group=c(rep('H6 GFP', 2), rep('HIF-2α', 2), rep('HIF-1α', 2)))

# In this case, need to remove the ".1", etc. in order to be able to merge with annotation file

mfcovington

#!/usr/bin/env sh
# Count reads and validate FASTQ files

FASTQ_DIR="$1"

if [ -z ${FASTQ_DIR+x} ]; then
    echo "Usage: $0 /path/to/fastq/files/"
    exit 1
fi

mfcovington

################################
# Auto-merge by sample and end #
################################

BASE_DIR=/Volumes/seagate/giriget

for SAMPLE in {1..144}; do
    for END in R1 R2; do

        # Gather files to process

mfcovington

[
  {
    sampleId: "CMMC001_33",
    lane: 2,
    barcode: "AACAGGCG",
    clusters: 3681934
  },
  {
    sampleId: "CMMC001_33",
    lane: 3,

mfcovington

from openpyxl import load_workbook


wb = load_workbook(filename = 'SubmissionForm.xlsx')
sheet = wb.get_sheet_by_name(wb.sheetnames[0])
header_row = sheet.rows[0]

for row in sheet.rows[1:]:

    # Ignore empty rows 

mfcovington

I'm in the process of making a CMS for scientific research labs. Our lab does a lot of genome/transcriptome sequencing and bioinformatic analyses. Therefore, I've been creating apps that would be useful for a scientific lab in general as well as one with our focus. I chose to build these upon django CMS to give extra flexibility in the both site design and the way the lab members interact with/edit the content.

There are a few integral apps still in the pipeline, but below are the ones that are in a usable state (although they do vary in terms of completeness). Once I've made sufficient progress, I plan on writing up a manuscript to submit to a scientific journal, because I believe that this type of site could be very useful for many labs. The project that I have incorporated these apps into is djangocms-lab-site.

• django CMS apps:

• djangocms-lab-members (Live App - [GitHub](https://github.com/mfcovi

mfcovington

REPOS_DIR=~/git.repos

for DIR in find $REPOS_DIR/* -maxdepth 0 -type d; do
    cd $DIR
    NEEDS_PUSH=`git rev-list develop...origin/develop --count`
    if [ "$NEEDS_PUSH" -gt 0 ]; then
        echo $DIR >> ~/repos-that-need-pushed
    fi
done