CREMA

Genes & Genomes
Systems Biology
Software tool

CREMA is an online tool which automatically infers regulatory networks from chromatin accessibility (ATAC/DNase-seq) or enhancer mark (ChIP-seq) data. CREMA directly processes raw data of a set of samples (FASTQ files), identifies cis-regulatory elements (CREs) , infers key transcription factors driving the observed chromatin state changes across the experimental conditions, and makes detailed predictions regarding their regulatory roles.

Browse the resource website

You might also be interested in

- Genomics
  , Transcriptomics
- Proteins & Proteomes
- Systems Biology
- Software tool
ISMARA

Webservice for gene expression and epigenetic data analysis
- Transcriptomics
- Systems Biology
- Software tool
DWT-online

Dinucleotide Weight Tensor toolbox and visualisation service
- Genomics
- Software tool
MADAP

Clustering tool of genomic sites
- Genomics
- Software tool
ChIP-Seq

ChIP-Seq data analysis tools
- Systems Biology
- Transcriptomics
  , Genomics
- Software tool
CRUNCH

Automated pipe-line for ChIP-seq data analysis
- Genes & Genomes
  , Genomics
  , Transcriptomics
- Evolution & Phylogeny
- Systems Biology
- Database
- Software tool
SwissRegulon Portal

Tools and data for regulatory genomics
- Transcriptomics
  , Genomics
- Systems Biology
- Database
SwissRegulon

Database of genome-wide annotations of regulatory sites
- Genomics
- Database
EPD

Eukaryotic Promoter Database
- Genomics
- Population genetics
  , Evolution biology
- Software tool
Nextclade

Clade assignment, mutation calling & QC for virus sequences
- Genomics
  , Transcriptomics
- Software tool
QuasR

Quantification and analysis of Short Reads