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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Database by Medisapiens Ltd. as fully integrated and annotated human gene expression data source. All genes are comparable across all samples. Provides data analysis options using database of human transcriptome.
Proper citation: IST Online (RRID:SCR_018794) Copy
https://vertebrate.genenames.org/
Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.
Proper citation: VGNC (RRID:SCR_017514) Copy
https://web.stanford.edu/group/dlab/optogenetics/
Database of different optogenetics resources like hardware, protocols, sequence information.
Proper citation: Optogenetics Resource Center (RRID:SCR_017513) Copy
https://github.com/hash-bang/Reflib-Node
Reference library processing for JavaScript. Reference library processing for NodeJS.
Proper citation: RefLib (RRID:SCR_018320) Copy
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
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
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
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
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
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
Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
Proper citation: Bioconductor (RRID:SCR_006442) Copy
A protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis.
Proper citation: MS Bioworks (RRID:SCR_001043) Copy
http://www.worm.mpi-cbg.de/phenobank/cgi-bin/ProjectInfoPage.py
A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens.
Proper citation: PhenoBank (RRID:SCR_000930) Copy
Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists.
Proper citation: Neuroscience Gateway (RRID:SCR_008915) Copy
Ratings or validation data are available for this resource
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.
Proper citation: Trim Galore (RRID:SCR_011847) Copy
Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework.
Proper citation: Apache Spark (RRID:SCR_016557) Copy
https://github.com/facebook/prophet
Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton.
Proper citation: Prophet (RRID:SCR_017083) Copy
Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations.
Proper citation: Data Biosphere (RRID:SCR_016154) Copy
https://github.com/TeamMacLean/atacr
Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes.
Proper citation: atacr (RRID:SCR_016286) Copy
https://github.com/kstreet13/slingshot
Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.
Proper citation: Slingshot (RRID:SCR_017012) Copy
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