C

Computational Analysis of gene Family Evolution (CAFE)

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing.

CAP3: A DNA sequence assembly program

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Includes

The CCP-EM software suite is a package containing tools for cryo-EM, including:

Clusters and compares protein or nucleotide sequences

CEAS: Cis-regulatory Element Annotation System

Cellpose, a generalist algorithm for cell and nucleus segmentation

A set of analysis pipelines that perform sample demultiplexing, V(D)J transcript sequence assembly and annotation, gene expression and feature barcode analysis from Single Cell Immune Profiling data.

Efficient genotyping bi-allelic SNPs on single cells

Classifier for metagenomic sequences.

Characterization of Germline variants

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Assess the quality of metagenome-assembled viral genomes.

UCSF Chimera - An extensible molecular modeling system

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI)

ChIP-R is a method for assessing the reproducibility of replicated ChIP-seq or ATAC-seq experiments.

a software for learning and characterizing chromatin states

circlator: a tool to circularise genome assemblies

Circos is a software package for visualizing data and information. It visualizes data in a circular layout

circos-tools provides several utility add-on scripts, such as for bundling links

cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

Efficient inferencing of recombination in bacterial genomes

Latest version of Clustal: a multiple sequence alignment program for DNA or proteins

Multiple alignment of nucleic acid and protein sequences

Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.

Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data

Copy number variant detection from high-throughput sequencing

A metapackage to obtain compilers

Clustering cONtigs with COverage and ComposiTion

an open source package management system and environment management system

Detect intra- and inter-species bacterial contamination in NGS reads

Conterminator: software to detect contamination in large sequence sets

A versatile tool to perform pile-up analysis on Hi-C data in .cool format (https://github.com/mirnylab/cooler). And who doesn't like cool pupppies?

Analysis tools for genomic interaction data stored in .cool format

Include:

The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.

CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications

A cowsay clone for python in one file.

Quantum chemistry and solid state physics software package

CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies.

Deep neural networks for continuous heterogeneous cryo-EM reconstruction

Deep learning particle picking procedure based YOLO.

CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.

CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.

The Cambridge Structural Database Software package (CSD-Software or CSDS) provides ConQuest, enCIFer, Gold, Hermes, Mercury and Mogul

A suite of command-line tools for working with CSV, the king of tabular file formats

programs for finding CTFs of electron micrographs

NVIDIA CUDA Toolkit provides a development environment for creating high performance GPU-accelerated applications

CUDA Toolkit - Including CUDA runtime

NVIDIA's cuDNN deep neural network acceleration library

Transcriptome assembly and differential expression analysis for RNA-Seq.

CulebrONT is an open-source, scalable, modular and traceable Snakemake pipeline, able to launch multiple assembly tools in parallel, giving you the possibility of circularise, polish, and correct assemblies, checking quality. CulebrONT can help to choose the best assembly between all possibilities.

tool and library for transferring data with URL syntax

Trim adapters from high-throughput sequencing reads

cuteSV is a long-read based human genomic structural variation detection tool

Cytoscape: an open source platform for network analysis and visualization.

A cytoskeleton simulation engine