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chromhmm

chromstar

Combinatorial and differential ChIP-seq analysis in R

clonealign

Bayesian inference of clone-specific gene expression estimates by assigning single-cell RNA-seq to clones

clust

Automatic and optimised consensus clustering of one or more heterogeneous datasets

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

clustree

Visualise Clusterings at Different Resolutions

cn_learn

CN-Learn

cnmf

Code and example data for funning Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

cnnc

covolutional neural network based coexpression analysis

cnvkit

Copy number variant detection from targeted DNA sequencing

coac

SingleCellSeqProject

colon_microbiopsies

Code and files accompanying article "The landscape of somatic mutation in normal colorectal epithelial cells"

conics

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing

conos

Clustering on Network of Samples

conquer

consistent quantification of external RNA-seq data sets

coop

Fast covariance, correlation, and cosine similarity.

coronary-progenitor-scrnaseq

coscape

Uncovering a unified single-cell coexpression landscape

couplenmf

cpg_me

A whole-genome bisulfite sequencing (WGBS) pipeline for the analysis and QC of DNA methylation that goes from from raw reads to a CpG count matrix

crc_code

Bioinformatics analysis code.

csn

Cell-specific Network Constructed by Single-cell RNA Sequencing Data

cytometry-clustering-comparison

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

dbscan

Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms - R package

dca

Deep count autoencoder for denoising scRNA-seq data

deepimpute

An accurate and efficient deep learning method for single-cell RNA-seq data imputation

deeptools

Tools to process and analyze deep sequencing data.

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

destin

destiny

R package for single cell and other data analysis using diffusion maps