SwissRegulon Portal

- Proteins & Proteomes

- Software tool

pftools

Build, calibrate, and search biological sequences

- Metagenomics

- Software tool

mVIRs

Prediction tool for inducible, bacteria-infecting viruses

- Transcriptomics

- Software tool

QuasR

Quantification and analysis of Short Reads

- Genomics

- Software tool

SSA

Analysis of nucleic acid sequence motifs

- Transcriptomics
- Systems Biology

- Software tool

ISMARA

Webservice for gene expression and epigenetic data analysis

- Genes & Genomes
- Systems Biology

- Software tool

CREMA

Cis-Regulatory Element Motif Activities

- Transcriptomics
- Systems Biology

- Software tool

DWT-online

Dinucleotide Weight Tensor toolbox and visualisation service

- Transcriptomics
- Systems Biology

- Database

SwissRegulon

Database of genome-wide annotations of regulatory sites

- Proteins & Proteomes

- Database

UniProtKB/Swiss-Prot

Protein knowledgebase

- Systems Biology

- Software tool

OMAMO

OMAMO allows the user to find the best simple model organism

- Transcriptomics
- Systems Biology

- Software tool

CRUNCH

Automated pipeline for ChIP-seq data analysis

- Proteins & Proteomes

- Database

UniProt SPARQL endpoint

SPARQL access to UniProt and related data

- Transcriptomics

- Database

PolyAsite

Database of curated RNA polyadenylation sites

- Genomics

- Database
- Software tool

EPD

Eukaryotic Promoter Database

- Transcriptomics

- Database
- Software tool

ASAP

Web-based, cooperative portal for single-cell data analyses

- Systems Biology

- Database

Cellosaurus

Knowledge resource on cell lines

- Systems Biology

- Database

Cellosaurus SPARQL endpoint

SPARQL access to Cellosaurus

- Transcriptomics
- Evolution biology

- Database
- Software tool

Bgee

Gene expression expertise

- Transcriptomics
- Evolution biology

- Database

Bgee SPARQL endpoint

SPARQL access to the Bgee gene expression database

- Proteins & Proteomes
- Systems Biology

- Database
- Software tool

STRING

Protein-protein interaction networks and enrichment analysis

- Proteins & Proteomes

- Database

UniProtKB

Protein sequence database

- Evolution & Phylogeny

- Database
- Software tool

OMA

Orthology inference among complete genomes

- Evolution & Phylogeny

- Database

OMA SPARQL endpoint

SPARQL access to the OMA Orthology database

- Evolution & Phylogeny

- Database

OrthoDB

Ortholog evolutionary and functional annotations

- Evolution & Phylogeny

- Database

OrthoDB SPARQL endpoint

SPARQL access to the OrthoDB catalog of orthologs

- Proteins & Proteomes
- Structural Biology

- Database

SWISS-MODEL Repository

Protein structure homology models

- Proteins & Proteomes
- Glycomics

- Database

GlyConnect

Integrated data platform to study glycosylation

- Proteins & Proteomes
- Glycomics

- Database

UniLectin

Structural and functional classification of lectins

- Proteins & Proteomes
- Glycomics

- Database

MatrixDB

Extracellular proteins and polysaccharides interactions

- Proteins & Proteomes

- Database
- Software tool

PaxDb

Protein abundance across several organisms

- Genes & Genomes
- Evolution & Phylogeny

- Database
- Software tool

SwissOrthology

One-stop shop for orthologs

- Structural Biology

- Database

ModelArchive

Repository of predicted macromolecular structure models

- Transcriptomics

- Software tool

miRmap

Prediction of microRNA target repression strength

- Genomics
- Evolution biology

- Database

Selectome

Database of positive selection

- Proteins & Proteomes
- Metabolomics

- Database
- Software tool

MetaNetX

Metabolic network repository & analysis

- Proteins & Proteomes
- Metabolomics

- Database

MetaNetX SPARQL endpoint

SPARQL access to MetaNetX

- Proteins & Proteomes

- Database

ABCD

Database of chemically defined antibodies

- Transcriptomics

- Software tool

TagScan

Genome-wide sequence tag scanner

- Transcriptomics

- Database
- Software tool

Fly Cell Atlas

Single-cell transcriptomes of the entire adult Drosophila

- Transcriptomics
- Proteins & Proteomes
- Systems Biology

- Software tool

NOODAI

Multi-omics data analysis and integration

- Genes & Genomes
- Proteins & Proteomes

- Software tool

MetaGraph

Petabase-scale sequence search

- Proteins & Proteomes
- Evolution & Phylogeny

- Database
- Software tool

Orthology Benchmarking

Quest for Orthologs benchmarking service

- Genomics

- Software tool

MADAP

Clustering tool of genomic sites

- Genomics

- Database
- Software tool

ChIP-Seq

ChIP-Seq data analysis tools

- Genomics
- Systems Biology

- Software tool

Phylogibbs

Regulatory sites in a collection of DNA sequences

- Genomics

- Database
- Software tool

SNP2TFBS

Regulatory SNPs affecting TF binding site affinity

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