Purdue University

Quast is Quality Assessment Tool for Genome Assemblies.

QuickMIRSeq is an integrated pipeline for quick and accurate quantification of known miRNAs and isomiRs by jointly processing multiple samples.

CellChat: Inference and analysis of cell-cell communication.

r-rnaseq is a customerized R module based on <code>R/4.1.1</code> used for RNAseq analysis.

r-scrnaseq is a customerized R module based on <code>R/4.1.1</code> or <code>R/4.2.0</code> used for scRNAseq analysis.

Racon is a consensus module for raw de novo DNA assembly of long uncorrected reads.

Ragout is a tool for chromosome-level scaffolding using multiple references.

Ragtag is a tool for fast reference-guided genome assembly scaffolding.

The RAPIDS suite of software libraries gives you the freedom to execute end-to-end data science and analytics pipelines entirely on GPUs. It relies on NVIDIA® CUDA® primitives for low-level compute optimization, but exposes that GPU parallelism and high-bandwidth memory speed through user-friendly Python interfaces.

RapMap is a testing ground for ideas in quasi-mapping and selective alignment.

Rasusa: Randomly subsample sequencing reads to a specified coverage.

Raven-assembler is a de novo genome assembler for long uncorrected reads.

Raxml (Randomized Axelerated Maximum Likelihood) is a program for the Maximum Likelihood-based inference of large phylogenetic trees.

Raxml-ng is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.

Reapr is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads.

Rebaler is a program for conducting reference-based assemblies using long reads.

The reciprocal smallest distance (RSD) algorithm accurately infers orthologs between pairs of genomes by considering global sequence alignment and maximum likelihood evolutionary distance between sequences.

Recycler is a tool designed for extracting circular sequences from de novo assembly graphs.

Regtools are tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.

RELION for REgularized LIkelihood OptimizatioN implements an empirical Bayesian approach for analysis of electron cryo-microscopy Cryo-EM. Specifically it provides methods of refinement of singular or multiple 3D reconstructions as well as 2D class averages. RELION is an important tool in the study of living cells.