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https://ualr.edu/bioinformatics/midsouth-bioinformatics-center/

Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice.

Proper citation: University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility (RRID:SCR_017168) Copy   

•   Source: SciCrunch Registry
  

https://www.hmtvar.uniba.it

Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information.

Proper citation: HmtVar (RRID:SCR_017288) Copy   

•   Source: SciCrunch Registry
  

http://epsd.biocuckoo.org/

Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies.

Proper citation: EPSD Eukaryotic Phosphorylation Site Database (RRID:SCR_016514) Copy   

•   Source: SciCrunch Registry
  

http://s-quest.bihealth.org/fiddle/

Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community.

Proper citation: fiddle (RRID:SCR_017327) Copy   

•   Source: SciCrunch Registry
  

http://www.mrmatlas.org/

Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome.

Proper citation: SRMAtlas (RRID:SCR_016996) Copy   

•   Source: SciCrunch Registry
  

http://www.humphreyslab.com/SingleCell/

Software tool as analyzer for kidney single cell datasets. Allows users to query gene expression from mouse or human kidney and human kidney organoid single cell datasets. For details about datasets visit ReBuilding a Kidney website.

Proper citation: Kidney Interactive Transcriptomics (RRID:SCR_017209) Copy   

•   Source: SciCrunch Registry
  

http://bloodexposome.org

Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields.

Proper citation: Blood Exposome Database (RRID:SCR_017610) Copy   

•   Source: SciCrunch Registry
  

https://www.genome.jp/kegg/pathway.html

Reference database for pathway mapping in KEGG Mapper. Collection of manually drawn pathway maps representing knowledge on molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organisms systems, human diseases, drug development.

Proper citation: KEGG PATHWAY Database (RRID:SCR_018145) Copy   

•   Source: SciCrunch Registry
  

https://www.cellphonedb.org/

Collection of publicly available data of curated receptors, ligands and their interactions. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand or receptor or to interrogate single cell transcriptomics data.

Proper citation: CellPhoneDB (RRID:SCR_017054) Copy   

•   Source: SciCrunch Registry
  

https://www.alzforum.org/alzpedia

Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge.

Proper citation: ALZPEDIA (RRID:SCR_017548) Copy   

•   Source: SciCrunch Registry
  

http://mimic.physionet.org/

Collection of comprising deidentified health related data associated with patients who stayed in critical care units of Beth Israel Deaconess Medical Center between 2001 and 2012. Database includes information such as demographics, vital sign measurements made at bedside (~1 data point per hour), laboratory test results, procedures, medications, caregiver notes, imaging reports, and mortality (both in and out of hospital).

Proper citation: Medical Information Mart for Intensive Care-III (RRID:SCR_017384) Copy   

•   Source: SciCrunch Registry
  

https://brads.nichd.nih.gov/Home/

Access to data from the Division of Intramural Population Health Research (DIPHR) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) from completed studies, including biospecimens and ancillary data.

Proper citation: Biospecimen Repository Access and Data Sharing (RRID:SCR_017383) Copy   

•   Source: SciCrunch Registry
  

https://dhs.ccm.sickkids.ca/

Collection of open chromatin regions from sequencing data. Metadata as entire curated DNase-I hypersensitive sites (DHS) on the whole genome datasets and data specific to each chromosome.

Proper citation: Database of Open Chromatin Regions (RRID:SCR_016614) Copy   

•   Source: SciCrunch Registry
  

http://10kimmunomes.org

Collection of reference datasets for human immunology, derived from control subjects in the NIAID ImmPort database . Available data include flow cytometry, CyTOF, multiplex ELISA, gene expression, HAI titers, clinical lab tests, HLA type, and others.

Proper citation: The 10000 Immunomes (RRID:SCR_016624) Copy   

•   Source: SciCrunch Registry
  

http://structuralbiology.cau.edu.cn/PlantGSEA/

Websever for gene set enrichment analysis of plants. Used for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets.

Proper citation: PlantGSEA (RRID:SCR_016866) Copy   

•   Source: SciCrunch Registry
  

http://larrywswanson.com/

Atlas with global nervous system nomenclature ontology and flatmaps for structure of rat brain. Open access resource for neuroscience community.

Proper citation: Brain Maps (RRID:SCR_017314) Copy   

•   Source: SciCrunch Registry
  

http://omicslab.genetics.ac.cn/dred/index.php

Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest.

Proper citation: Database of genes related to Repeat Expansion Diseases (RRID:SCR_018086) Copy   

•   Source: SciCrunch Registry
  

http://www.mqtldb.org/

Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES).

Proper citation: mqtldb (RRID:SCR_018002) Copy   

•   Source: SciCrunch Registry
  

https://www.postgresql.org/

Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems.

Proper citation: PostgreSQL (RRID:SCR_021067) Copy   

•   Source: SciCrunch Registry
  

https://www.tfcheckpoint.org/

Collection of transcription factors annotated according to experimental and other evidence on their function as true DbTFs. Provides reference for both small scale experiments and genome scale studies. Curated compendium of specific DNA-binding RNA polymerase II transcription factors.

Proper citation: tfcheckpoint (RRID:SCR_023880) Copy   

•   Source: SciCrunch Registry