Building R Packages

Hands On Load Required Packages # devtools automates some of the setup for a new package library(devtools) # roxygen2 handles building the documentation library(roxygen2) Define Some Variables # Define package directory package_wd <- “/home/mk5636/badas-r-package” # Define package name as string package_name <- ‘badas’ Create A Package Skeleton Using create() dir.create(file.path(package_wd)) setwd(file.path(package_wd)) # The ‘create’ function … Continue reading Building R Packages

Intro to Nextflow

Hands On The figure below depicts the simple pipeline we will build. Note the dependencies (indicated with arrows) and the steps which run in parallel (same row). Launch interactive sessionsrun -c2 -t1:00:00 –mem=10000 –pty /bin/bash Load nextflowmodule load nextflow/20.01.0 Make the config fileparams.reads = “/scratch/mk5636/nextflow-badas/data/*.fastq.gz”params.ref = “/scratch/work/cgsb/genomes/Public/Fungi/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa”params.out = “$SCRATCH/nextflow-badas/out”workDir = params.out + ‘/nextflow_work_dir’ Building the … Continue reading Intro to Nextflow

JBrowse: Visualizing Data Quickly & Easily

Watch the September 24, 2020 BADAS here. Introduction During the 2020 Summer of COVID-19, the Ghedin and Gresham labs sequenced SARS-CoV-2 isolates. To visualize and share this data with collaborators the web-based genome visualization software JBrowse was used To benefit all researchers at NYU engaged in genomics research, a centralized JBrowse service has been … Continue reading JBrowse: Visualizing Data Quickly & Easily

Nextflow + Containerization

Presented by: Tobias Schraink and Stephen Kelly March 28, 2019 Prerequiste Nextflow Nextflow hands-on Step 1: Define the pipeline parameters Step 2: Create transcriptome index file Step 3: Collect read files by pairs Step 4: Perform expression quantification Step 5: Quality control Step 6: MultiQC report Step 7: Handle completion event Step 8: Custom scripts … Continue reading Nextflow + Containerization

Containerization with Docker

BADAS Slides Installation To view detailed installation instructions you may visit the Docker website. For this tutorial we have taken out much of the details and provided you with the commands you will most likely need. MacOS All you need is to download the dmg here. Alternatively you will need to visit the Docker Hub … Continue reading Containerization with Docker

Jupyter Notebook

Jupyter notebooks are a very useful tool for sharing data and analyses. They are essentially an interactive coding environment that is feature rich and has very useful and practical integrations. Some examples of notebooks that have been used in place of materials and methods sections can be found here. These are good reference materials for … Continue reading Jupyter Notebook

Regular Expressions

A regular expression (aka regex) is a sequence of characters that describe or match a pattern of text. For example, the string aabb12 could be described as aabb12, two a’s, two’bs, then 1, then 2, or four letters followed by two numbers. Keep in mind that regular expressions differ slightly per language but the theort … Continue reading Regular Expressions