Expasy: Swiss Bioinformatics Resource Portal
e.g. BLAST, UniProt, MSH6, Albumin...

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
      • 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
      • Genes & Genomes
      • , Genomics
      • , Transcriptomics
      • Evolution & Phylogeny
      • Systems Biology
      • Database
      • Software tool

    SwissRegulon Portal

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

    SwissRegulon

    Database of genome-wide annotations of regulatory sites
      • Systems Biology
      • Software tool

    OMAMO

    OMAMO allows the user to find the best simple model organism
      • Genomics
      • , Transcriptomics
      • Systems Biology
      • Software tool

    CRUNCH

    Automated pipeline for ChIP-seq data analysis
      • Genomics
      • Software tool

    MADAP

    Clustering tool of genomic sites
      • Genomics
      • Software tool

    ChIP-Seq

    ChIP-Seq data analysis tools
      • Genomics
      • Systems Biology
      • Software tool

    Phylogibbs

    Regulatory sites in a collection of DNA sequences
      • Transcriptomics
      • Software tool

    ASAP

    Web-based, cooperative portal for single-cell data analyses
      • Text mining & Machine learning
      • Database
      • Software tool

    SIBiLS

    Personalized information retrieval from the literature
      • Genomics
      • Evolution & Phylogeny
      • Software tool

    Nextclade

    Clade assignment, mutation calling & QC for virus sequences
      • Genomics
      • Population genetics
      • Software tool

    V-pipe

    Viral genomics pipeline
      • Evolution & Phylogeny
      • Software tool

    raxmlGUI

    raxmlGUI 2.0 is a graphical user interface to RAxML
      • Proteins & Proteomes
      • Structural Biology
      • , Structural analysis
      • Software tool

    SWISS-MODEL Workspace

    Fully automated protein structure homology-modeling server
      • Proteins & Proteomes
      • Database
      • Software tool

    HAMAP

    UniProtKB family classification and annotation
      • Genes & Genomes
      • Evolution & Phylogeny
      • Software tool

    REALPHY

    Inference of phylogenetic trees from genome data
      • Genomics
      • Population genetics
      • Software tool

    V-pipe SARS-CoV-2

    V-pipe pipeline for SARS-CoV-2 sequencing data
      • Genomics
      • Evolution biology
      • Software tool

    Nextstrain

    Impact of pathogen genome data on science and public health
      • Genomics
      • Software tool

    ShoRAH

    Analysis of NGS data
      • Structural analysis
      • Software tool

    OpenStructure

    Molecular modelling and visualisation environment
      • Metagenomics
      • Software tool

    LEMMI

    Continuous benchmarking of methods for metagenomics
      • Medicinal chemistry
      • , Structural analysis
      • Software tool

    SwissParam

    Topology and parameters for small molecules
      • Proteins & Proteomes
      • Structural Biology
      • Database
      • Software tool

    CAMEO

    Weekly automated benchmarking of protein structure modelling
      • Genomics
      • , Transcriptomics
      • Software tool

    QuasR

    Quantification and analysis of Short Reads