Software
The Bioinformatics team focuses on the development of Bioinformatics software for high-throughput analysis, quality control and visualization of biological data relevant to our work at the Rockefeller University. All sofware developed is publically available through our github site or from online, peer-reviewed repositories. We currently maintain 3 analysis pipelines (Basecalling, ChIP-seq and RNA-seq) available on our Github site, to allow for the rapid and reproducible processing and initial analysis of these common data types. We also developed and maintain five Bioconductor packages within the team: profileplyr, basecallQC, ChIPQC, tracktables and soGGi.
ChIPQC (Bioconductor package)
Developed by Tom Carroll, Rockefeller University, with Rory Stark at CRUK, ChIPQC provides a set of tools for the evaluation of ChIP-seq, MNAse-seq and ChIP-exo quality Bioconductor Site:- Link Bioconductor talk/course on ChIPQC:- Link Related paper:- Link
tracktables (Bioconductor package)
Developed by Tom Carroll at the Rockefeller University, tracktables provides tools to create dynamic genome browser linked (IGV) HTML reports from BAM, bigwigs and interval files as well as many Bioconductor objects. Bioconductor Site:- Link Github Site:- Link
soGGi (Bioconductor package)
Developed by Tom Carroll and Doug Barrows at the Rockefeller University, soGGi (summarising over grouped genomic intervals) provides tools to summarise and visualise signal, motifs and conservation over genomic ranges using GGplot2. Bioconductor Site:- Link Github Site:- Link
profileplyr (Bioconductor package)
Developed by Doug Barrows and Tom Carroll at the Rockefeller University, profileplyr provides a framework for working with genomic heatmaps from R and Deeptools software Bioconductor Site:- . Link Github Site:-Link Doug's workflow:-Link
Rfastp (Bioconductor package)
Developed by Wei Wang and Tom Carroll at the Rockefeller University, Rfastp provides ultrafast FastQ handling and QC Bioconductor Site:- . Link Github Site:-Link
Herper (Bioconductor package)
Developed by Matt Paul and Tom Carroll at the Rockefeller University, Herper provides a framework for working with Conda environments in an R environments Bioconductor Site:- . Link Github Site:-Link
Infrastructure
On top of the publically available software created and maintained by the Rockefeller University Bioinformatics Resource Center team, the team develops pipelines and infrastructure for the required high throughput processing, quality control and initial analysis of high throughput biological data created within the Rockefeller University as well maintain our course materials.
- Basecalling - Automated basecalling, demulitplexing, FastQC and simple statistics
- ChIP-seq - Automated alignment, ChIPQC, BigWigs, peakcalling, motif identification and differential bindind analysis
- RNA-seq - Automated alignment, RNAseq-QC, bigWigs, counting in genes, differential expression analysis