Purdue University

Chromap is an ultrafast method for aligning and preprocessing high throughput chromatin profiles.

CICERO (Clipped-reads Extended for RNA Optimization) is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq.

CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization.

Circlator is a tool to circularize genome assemblies.

CirComPara2 is a computational pipeline to detect, quantify, and correlate expression of linear and circular RNAs from RNA-seq data that combines multiple circRNA-detection methods.

Circos is a software package for visualizing data and information.

CIRI2: Circular RNA identification based on multiple seed matching.

CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data.

Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.

Clairvoyante is a deep neural network based variant caller.

ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise.

Clever-toolkit is a collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads. The main software is written in C++ with some auxiliary scripts in Python.

ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes.

Clust is a fully automated method for identification of clusters (groups) of genes that are consistently co-expressed (well-correlated) in one or more heterogeneous datasets from one or multiple species.

Clustalw is a general purpose multiple alignment program for DNA or proteins.

A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

CNVkit is a command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.

Cnvnator is a tool for discovery and characterization of copy number variation (CNV) in population genome sequencing data.

Coinfinder is an algorithm and software tool that detects genes which associate and dissociate with other genes more often than expected by chance in pangenomes.

Comsol Multiphysics (previously named Femlab) is a modeling package for the simulation of any physical process you can describe with partial differential equations (PDEs).