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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.
Registry for source codes of interest to astronomers and astrophysicists, including solar system astronomers, and lists codes that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. ASCL is indexed by SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net .
Proper citation: Astrophysics Source Code Library (RRID:SCR_017604) Copy
https://sourceforge.net/projects/bva-io/
Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.
Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy
https://github.com/AllenInstitute/scrattch.hicat
Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute.
Proper citation: Scrattch.Hicat (RRID:SCR_018099) Copy
https://gitlab.com/biomerieux-data-science/clustlasso
Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach.
Proper citation: clustLasso (RRID:SCR_018820) Copy
https://github.com/quest-bih/oddpub
Text mining algorithm to screen biomedical publications to find data sharing statements. Algorithm that parses set of publications and detects which publications disseminated Open Data or Open Code together with publication. Tailored towards biomedical literature.
Proper citation: ODDPub (RRID:SCR_018385) Copy
https://github.com/aertslab/SCENIC
Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data.
Proper citation: SCENIC (RRID:SCR_017247) Copy
Platform for Secure Access to Research Data and E-Infrastructure based on European Standards for Health Case information. Used for secure processing of sensitive personal data in research in health and care sector.
Proper citation: Secure Access to Research Data and E-Infrastructure (RRID:SCR_017246) Copy
https://sciex.com/products/software/lipidview-software
Software tool for molecular characterization and quantification of lipid species from electrospray mass spectrometry data. Enables lipid profiling by searching parent and fragment ion masses against lipid fragment database and reports numerical and graphical output for various lipid molecular species, lipid classes, fatty acids, and long chain bases.
Proper citation: LipidView Software (RRID:SCR_017003) Copy
https://gitlab.com/KHanghoj/DamMet
Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.
Proper citation: DamMet (RRID:SCR_016959) Copy
Open source resources to execute stop signal task and analyze resulting data. Simulation code is provided, and can be used in planning stage for investigation of response inhibition and impuls control.
Proper citation: stop-signal task resources (RRID:SCR_017137) Copy
https://github.com/bids-standard/bids-validator
Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure.
Proper citation: BIDS Validator (RRID:SCR_017255) Copy
https://hub.docker.com/r/mziemann/tallyup/
Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript.
Proper citation: Digital Expression Explorer 2 Docker Image (RRID:SCR_016931) Copy
http://ophid.utoronto.ca/mirDIP/
microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies.
Proper citation: mirDIP (RRID:SCR_016770) Copy
https://www.schrodinger.com/maestro
Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data.
Proper citation: Maestro (RRID:SCR_016748) Copy
http://cab.spbu.ru/software/rnaquast/
Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.
Proper citation: rnaQUAST (RRID:SCR_016994) Copy
http://www.nitrc.org/projects/brainlife_io/
Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain.
Proper citation: brainlife.io (RRID:SCR_016513) Copy
https://github.com/ropenscilabs/datastorr
Software package for simple data retrieval and versioning.
Proper citation: datastorr (RRID:SCR_017040) Copy
https://openknowledgemaps.org/
Software tool as an open source knowledge mapping software that increases the visibility of research findings for science and society. Visual interface to the world's scientific knowledge.
Proper citation: Open Knowledge Maps (RRID:SCR_016470) Copy
https://www.ncbi.nlm.nih.gov/genbank/wgs/
Project for assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. The nucleotide and protein data from all WGS projects go into the BLAST database.
Proper citation: Whole Genome Shotgun (WGS) Project (RRID:SCR_016637) Copy
https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
Software tool as a command-line program that automates the creation of sequence records for submission to GenBank. Records need no additional manual editing before submission.
Proper citation: tbl2asn (RRID:SCR_016636) Copy
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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