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Micro DNA identification

circm

Scripts for merging circRNA prediction output

circompara

A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

circscan

Discovering the Circular RNA Interactions with RNA-binding Proteins and Ribosomes

circview

Sample-specific CircRNA Viewer

ciriquant

circular RNA quantification tools

cisd

Chromatin Interaction Site Detector

cistopic

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

clubcpg

Cluster-based analysis of CpG methylation

cncdriver

codes3d

The CoDeS3D toolkit for combined analysis of HiC and eQTL data

collectiontools

Collection bioinformatics tools from public websites

colon-dna-topology

comet

The coMET package is a web-based plotting tool and R-based package to visualize different genome-wide association scans such as EWAS (epigenome-wide association scan) results in a genomic region of interest. coMET provides a plot of the EWAS association signal and visualisation of the methylation correlation between CpG sites (co-methylation). The coMET package also provides the option to annotate the region using functional genomic information, including both user-defined features and pre-selected features based on the Encode project. The plot can be customized with different parameters, such as plot labels, colours, symbols, heatmap colour scheme, significance thresholds, and including reference CpG sites. Finally, the tool can also be applied to display the correlation patterns of other genomic data, e.g. gene expression array data.

community

A Python implementation of Girvan-Newman community detection algorithm for weighted graphs

community_software_tools_for_ngs

complexheatmap

make complex heatmaps as well as self define annotation graphics

consensustme

ConsensusTME Gene Sets and R Script

cosopt

Bioinformatics / detection of periodic patterns in gene expression data

covid-19-rna-seq-datasets

A repository for sharing information on available COVID-19 RNA-Seq datasets

cpgcluster

Finding CpG islands in genome sequences

cream

CREAM (Clustering of Functional Regions Analysis Method) is a new method for identification of clusters of functional regions (COREs) within chromosomes.

credwards_gene_alias

Ensembl gene disambiguation

crisp

Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples

cross-organ_riboprof

Translational contributions to tissue-specificity in rhythmic and constitutive gene expression.

cworld-dekker

perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)

damage-estimator

dapars

DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)

dcc

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

deep-learning-papers-reading-roadmap

Deep Learning papers reading roadmap for anyone who are eager to learn this amazing tech!