LibGuides: Biomedical Big Data Resource Center: Database & Tools

Databases & Tools

HumanNet
A probabilistic functional gene network of 18,714 validated protein-encoding genes of Homo sapiens (by NCBI March 2007), constructed by a modified Bayesian integration of 21 types of 'omics' data from multiple organisms.
StringDb
GATHER
Gene Annotation Tool to Help Explain Relationships.

NCBI Gene
Clusters of Orthologous Groups (COGs)
Comprehensive Microbial Resource (CMR) Database
Ensembl Genome Browser
NCBI Genome (Entrez)
Gene Ontology (GO) Project
UCSC Genome Bioinformatics Site
NCBI Map Viewer
Integrated views of chromosome maps for many organisms. View assembled genomes, identify and localize genes and other biological features.
NCBI UniGene
Coremine Medical
Information about genes and proteins presented as "literature networks" based on instances where gene or protein names appear in articles together, providing a way to visualize possible direct or indirect connections (e.g., biological interactions).
GeneCards Human Gene Database
GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.
Information Hyperlinked Over Proteins (iHOP)
Information about genes and proteins hyperlinked via relevant words found in PubMed abstracts, creating a network of protein-related topics from the research literature.

DAVID Bioinformatics Resources 6.8 National Institute of Allergy and Infectious Diseases (NIAID), NIH
An older but powerful tool for calculating functional enrichment in gene lists.
Enrichr, by Ma’ayan Lab
Tool for calculating functional enrichment in gene lists.

Bioconductor
R packages for the life sciences, many of which focus on genomic analysis
Eigensoft: Software List @Harvard, by Alkes Price
The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and EIGENSTRAT stratification correction method (Price et al. 2006)
ApE - A plasmid Editor
A free, open source, used for manipulating nucleic acid sequences for molecular biology.
GATK; genome analysis toolkit, from the Broad Institute
Genome analysis toolkit from the Broad Institute:
Cytoscape
Use for mapping gene and protein interactions.
Segway
Helpful for annotating states across the genome.
ChromHMM
Software for learning and characterizing chromatin states.
QIIME (pronounced Chime)
Open source toolkit for microbial ecology
kallisto, @ Caltech by Pachter Lab
Program for quantifying abundances of transcripts from RNA-Seq data: it doesn’t require alignment to a genome, it uses a technique called “pseudoalignment” and is fast.
sleuth
Program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.

TAIR: The Arabidopsis Information Resource

Unlimited users.
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR include the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, and publications. Gene product function data is updated every week from the latest published research literature and community data submissions.

ChIP-seq validated antibodies

Literature

Roadmap epigenomics
Epigenetic information and experiments from healthy adult and fetal tissue.
Nature collection of Roadmap Epigenomics Articles
ENCODE
Link is main project page. Focus is on regulation of the genome, not sequence variation
Nature collection on the ENCODE project articles

dbSNP
Short genetic variations database by NCBI.
BreakDancer
BreakDancer, released under GPLv3, is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
Gerstein lab structural variation data and tools:
SVDetect
Software to detect structural variation in paired-end sequence data.

Affymetrix Probe Set in Tabular Format
Microarray technical documentation, part of the Thermo Fisher Scientific.
Affymetrix, HT Human Genome U133 Array Plate Set - Support Materials
Part of Thermo Fisher Scientific.
MAGE-TAB Format
Literature for MIAME-compliant microarray experiments.