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Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.
Proper citation: CIS-BP (RRID:SCR_017236) Copy
https://www.umass.edu/ials/pccl-database
Collection of plant species for use by both academia and industry.The PCCL enables R&D exploitation of monocot, dicot and gymnosperm cultures.
Proper citation: Plant Cell Culture Library (PCCL) (RRID:SCR_016784) Copy
https://wiki.helsinki.fi/display/twineng/Twinstudy
Twin panel consists of three nationwide samples of Finnish twin pairs. Major studies include nicotine dependence, eating disorders and brain imaging and alcohol use.
Proper citation: Finnish Twin Cohort Study (RRID:SCR_017477) Copy
http://clonesearch.jdrfnpod.org/
Database of sequence data generated from high-throughput immunosequencing of the TCR beta chain (TRB) and B cell receptor (BCR) immunoglobulin heavy chain (IGH). This data comes from cells from NPOD donors.
Proper citation: nPOD TCR/BCR Search (RRID:SCR_015851) Copy
http://mona.fiehnlab.ucdavis.edu
Metadata-centric, auto-curating repository designed for storage and querying of mass spectral records. It contains metabolite mass spectra, metadata and associated compounds.
Proper citation: MassBank of North America (RRID:SCR_015536) Copy
https://www.clinicalgenome.org
Genomics knowledgebase for clinical relevance of genes and variants for use in research. ClinGen's primary function is to store and share information for the benefit of the scientific community. Laboratory scientists, clinicians, and patients can share and access data.
Proper citation: ClinGen (RRID:SCR_014968) Copy
http://mirwalk.umm.uni-heidelberg.de/
Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets.
Proper citation: miRWalk (RRID:SCR_016509) Copy
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
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
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
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
It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets.
Proper citation: ROIs selection with a non-graphical user interface (RRID:SCR_016352) Copy
http://www.nitrc.org/projects/asdb/
Database as an open science framework with a scientific data extracted from scientific literature about various altered states of consciousness assessed with questionnaires. Used to compare what experiences are elicited by different drugs and non-pharmacological methods that induce altered states to help to understand human consciousness functions. Is listed by Neuroimaging Informatics Tools.
Proper citation: Altered States Database (RRID:SCR_016350) Copy
https://figshare.com/articles/phi_toolbox_zip/3203326
Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation.
Proper citation: Phi Toolbox (RRID:SCR_015549) Copy
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
http://bioconductor.org/packages/EGSEA/
Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.
Proper citation: EGSEA (RRID:SCR_015036) Copy
https://astrocyte.rnaseq.sofroniewlab.neurobio.ucla.edu
Database containing information about RNA-sequencing and astrocyte reactivity. Searching a gene through this engine provides differential expression data for various experimental conditions.
Proper citation: Astrocyte Reactivity RNA-Seq Browser (RRID:SCR_015033) Copy
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
Database and repository of tissues relating to mouse models of breast cancer. Users can search and share models, and members can enter details of available material to share on a collaborative basis.
Proper citation: SEARCHBreast (RRID:SCR_014826) Copy
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
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