Purdue University

RepeatMakser is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

RepeatModeler is a de novo transposable element (TE) family identification and modeling package.

RepeatScout is a tool to discover repetitive substrings in DNA.

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.

RevBayes -- Bayesian phylogenetic inference using probabilistic graphical models and an interactive language.

MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold

rmats2sashimiplot produces a sashimiplot visualization of rMATS output. rmats2sashimiplot can also produce plots using an annotation file and genomic coordinates. The plotting backend is MISO.

RNAIndel calls coding indels from tumor RNA-Seq data and classifies them as somatic, germline, and artifactual. RNAIndel supports GRCh38 and 37.

RNApeg is an RNA junction calling, correction, and quality-control package. RNAIndel supports GRCh38 and 37.

Rnaquast is a quality assessment tool for de novo transcriptome assemblies.

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome.

HPCG is a HPC benchmark intended to better represent computational and data access patterns that closely match a broad set of scientific workloads. This container implements the HPCG benchmark on top of AMDs ROCm platform.

HPL, or High-Performance Linpack, is a benchmark which solves a uniformly random system of linear equations and reports floating-point execution rate. This container implements the HPL benchmark on top of AMDs ROCm platform.

ROCm Application for Reporting System Info.

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

Rseqc is a package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.

RStudio is an integrated development environment (IDE) for the R statistical computation and graphics system.

This package installs Rstudio desktop from pre-compiled binaries available in the Rstudio website. The installer assumes that you are running on CentOS7/Redhat7/Fedora19. Please fix the download URL for other systems.

run_dbCAN using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

rush is a tool similar to GNU parallel and gargs. rush borrows some idea from them and has some unique features, e.g., supporting custom defined variables, resuming multi-line commands, more advanced embedded replacement strings.