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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.
Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data.
Proper citation: nelpy (RRID:SCR_016209) Copy
http://uthscsa-imagetool.software.informer.com/
Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images.
Proper citation: UTHSCSA ImageTool (RRID:SCR_016208) Copy
https://www.hiv.lanl.gov/catnap
Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712
Proper citation: CATNAP (RRID:SCR_016170) Copy
https://hub.docker.com/r/biodepot/star-for-criu/
Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability.
Proper citation: star-for-criu (RRID:SCR_016294) Copy
https://www.goldwave.com/goldwave.php
Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes.
Proper citation: GoldWave (RRID:SCR_016189) Copy
Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines.
Proper citation: Lifebit Deploit (RRID:SCR_016428) Copy
Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.
Proper citation: GOTrack (RRID:SCR_016399) Copy
https://www.denovosoftware.com/?gclid=EAIaIQobChMI36rn3-Dd3AIV2ud3Ch27lw2oEAAYASAAEgLbRvD_BwE
Software tool for flow and image cytometry data analysis by De Novo Software company.
Proper citation: FCS Express (RRID:SCR_016431) Copy
Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models.
Proper citation: Vensim (RRID:SCR_016394) Copy
Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users.
Proper citation: OmicsBean (RRID:SCR_016322) Copy
https://github.com/Sung-Huan/ANNOgesic
Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.
Proper citation: ANNOgesic (RRID:SCR_016326) Copy
https://www.genomics.agilent.com/article.jsp?pageId=2100
Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System.
Proper citation: MxPro QPCR (RRID:SCR_016375) Copy
http://bioconductor.org/packages/release/bioc/html/MetaCyto.html
Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.
Proper citation: MetaCyto (RRID:SCR_016415) Copy
https://deeptools.readthedocs.io/en/develop/
Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches.
Proper citation: Deeptools (RRID:SCR_016366) Copy
https://github.com/sblanck/smagexp
Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.
Proper citation: SMAGEXP (RRID:SCR_016360) Copy
https://github.com/mikessh/migec
Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires.
Proper citation: migec (RRID:SCR_016337) Copy
http://www.flir.jp/instruments/display/?id=54865
Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data.
Proper citation: FLIR tools (RRID:SCR_016330) Copy
Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi.
Proper citation: UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) Copy
http://www.nitrc.org/projects/mica/
Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.
Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy
Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.
Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy
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