RNASEQ20 required software

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RNASEQ20 Requirements
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• Hardware (64-bit computer running either Linux or Mac OS X (10.7 Lion or later); 4 GB of
RAM (8 GB preferred)

• Data (example RNA-seq reads, indexes and gene annotations for use in this protocol are
available at ftp://ftp.ccb.jhu.edu/pub/RNAseq_protocol ; see Equipment Setup for details)

• FASTQC ( https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ )
• HISAT2 software (http://ccb.jhu.edu/software/hisat2 or http://github.com/infphilo/hisat2,
version 2.0.1 or later), Not available on Windows, use Subread aligner from R package Rsubreads
• Kallisto https://pachterlab.github.io/kallisto/download
(https://bioconductor.org/packages/release/bioc/html/Rsubread.html)
• QualiMap (http://qualimap.bioinfo.cipf.es/) Not available on Windows: use NOISeqQC from R package NOIseq
• SAMtools (http://samtools.sourceforge.net, version 0.1.19 or later) Not available on Windows: use R package Rsamtools
• StringTie software (http://ccb.jhu.edu/software/stringtie or https://github.com/gpertea/stringtie,
version 1.2.2 or later) Not available on Windows, no alternative available

• R (https://www.r-project.org, version 3.2.2 or later)
• R package AnnotationHub (https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html)
• R package clusterProfiler (https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html)
• R package DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html)
• R package devtools (https://cran.r-project.org/web/packages/devtools/index.html)
• R package DOSE (https://bioconductor.org/packages/release/bioc/html/DOSE.html)
• R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html)
• R package ensembldb (https://bioconductor.org/packages/release/bioc/html/ensembldb.html)
• R package ggplot2 (https://cran.rstudio.com/web/packages/ggplot2/index.html)
• R package gridExtra (https://cran.r-project.org/web/packages/gridExtra/index.html)
• R package mixOmics (https://www.bioconductor.org/packages/release/bioc/html/mixOmics.html)
• R package NOIseq (https://bioconductor.org/packages/release/bioc/html/NOISeq.html)
• R package org.Mm.eg.db (http://bioconductor.org/packages/release/data/annotation/html/org.Mm.eg.db.html)
• R package pathview (https://bioconductor.org/packages/release/bioc/html/pathview.html)
• R package pheatmap (https://cran.r-project.org/web/packages/pheatmap/index.html)
• R package RColorBrewer (https://cran.r-project.org/web/packages/RColorBrewer/index.html)
• R package reshape2 (https://cran.r-project.org/web/packages/reshape2/index.html)
• R package Rsamtools https://bioconductor.org/packages/release/bioc/html/Rsamtools.html
• R package Rsubreads (https://bioconductor.org/packages/release/bioc/html/Rsubread.html)
• R package tidyverse (https://www.tidyverse.org/packages/)
• R package tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html)
• R package (https://bioconductor.org/packages/release/bioc/html/ballgown.html)