Commonly used software

Bioconductor

• Where do I start using Bioconductor? blog post by Leo.
• How to ask for help for Bioconductor packages blog post by Leo.
• Bioconductor workflows such as rnaseqGene and sequencing are very helpful to get started in the RNA sequencing (RNA-seq) field.
• BioC2019 workshops are available here.
• limma: is one of the main packages we use for analyzing data, particularly with the limma-voom method. Check the Bioconductor workflows that explain limma in more detail here.
• GenomicRanges: is the package we use for interacting with genomic data across ranges. Check the introduction for more information.
• SummarizedExperiment: is the package we use for creating and interacting with RangedSummarizedExperiment objects.
• bsseq: is highly useful for analyzing DNA methylation data, particularly whole genome bisulfite sequencing (WGBS) data.
• Biostrings: is useful for dealing with sequence information such as the human genome sequence.
• recount: contains the getRPKM function that we use frequently and allows accessing data from many human RNA-seq projects.
• derfinder: contains functions for BigWig files and other related RNA-seq methods.

Lab software

• jaffelab (documentation): contains several functions we’ve written over the years that we find helpful for different analyses.
• sgejobs (documentation): contains helper functions for writing and interacting with SGE jobs at JHPCE.
• jhpce_mod_source and jhpce_module_config are our GitHub repositories for our LIBD modules.
• libdRSE (documentation): is similar to recount for accessing coverage data from LIBD projects.
• shinycsv: allows interactively exploring a table.
• LIBDpheno: contains phenotype information for LIBD samples.
• recount.bwtool: is an R package for dealing with BigWig files using bwtool. Check also bamcount by Christopher Wilks.
• brainflowprobes: is an R package for designing flow probes written by Amanda J Price.
• LIBD RNA-seq processing pipeline: initial version and nextflow version.
• globus: our Globus share endpoints such that others can access our data.
• easyweb for easily creating your own personal R markdown website.

Writing papers

• How to write academic documents with GoogleDocs using F1000Workspace blog post. Check the original version for some additional information.