Purdue University

Cd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences.

Cdbtools is a collection of tools used for creating indices for quick retrieval of any particular sequences from large multi-FASTA files.

CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome.

Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression (GEX), chromatin accessibility, and their linkage. Furthermore, since the ATAC and GEX measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and GEX.

Cell Ranger DNA is a set of analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation (CNV), and compare heterogeneity among cells.

Cellbender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions.

Cellranger is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

Cellranger-atac is a set of analysis pipelines that process Chromium Single Cell ATAC data.

CellRank a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data.

CellRank a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. CellRank-krylov is <code>CellRank</code> installed with extra libraries, enabling it to have better performance for large datasets (>15k cells).

cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo, which assigns cells to donors and detects doublets, even without genotyping reference.

Celltypist is a tool for semi-automatic cell type annotation.

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers.

The CFSAN SNP Pipeline is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.

chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers.

Chopper is Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file. Filtering is done on average read quality and minimal or maximal read length, and applying a headcrop (start of read) and tailcrop (end of read) while printing the reads passing the filter.

The Chroma package provides a toolbox and executables to carry out calculation of lattice Quantum Chromodynamics LQCD. It is built on top of the QDP++ QCD Data Parallel Layer which provides an abstract data parallel view of the lattice and provides lattice wide types and expressions, using expression templates, to allow straightforward encoding of LQCD equations.