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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.
https://github.com/bbuchfink/diamond
Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.
Proper citation: DIAMOND (RRID:SCR_016071) Copy
http://acb.qfab.org/acb/glam2/
Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.
Proper citation: Glam2 (RRID:SCR_016129) Copy
Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization.
Proper citation: GenomeTools (RRID:SCR_016120) Copy
https://savannah.gnu.org/projects/datamash/
Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts.
Proper citation: Datamash (RRID:SCR_016067) Copy
Software that employs machine learning techniques and high-performance computing for analyzing task-based fMRI datasets. It applies Feature Analysis, Hyperalignment, Multi-voxel Pattern Analysis (MVPA), Representational Similarity Analysis (RSA), and more.
Proper citation: Easy fMRI (RRID:SCR_016392) Copy
https://gemma.msl.ubc.ca/phenotypes.html
Database that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. Part of Gemma, a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data.
Proper citation: Phenocarta (RRID:SCR_016273) Copy
Web based software for analyzing genomic variants CNVs, SNVs, and Indels and phenotypes. It aims to represent the relationships between discovered variants and phenotypes.
Proper citation: AspireDB (RRID:SCR_016272) Copy
https://www.ncbi.nlm.nih.gov/pubmed/23489480
Software package for image analysis to determine the orientation of filamentous structures on digital images. Used as an image‐processing tool for analyzing cytoskeleton and cellulose fiber orientation in pant imagesk.
Proper citation: MicroFilament Analyzer (RRID:SCR_016411) Copy
https://www.picoquant.com/products/category/software
Software for fluorescence lifetime imaging and correlation. SymPhoTime 64 is the data acquisition software for PicoQuant's time-resolved confocal microscope MicroTime 200 and LSM upgrade kits.
Proper citation: SymPhoTime 64 (RRID:SCR_016263) Copy
http://www.birds.cornell.edu/brp/raven/RavenOverview.html
Software for the acquisition, visualization, measurement, and analysis of sounds. Raven supports annotations for research-related analysis.
Proper citation: Raven (RRID:SCR_016190) Copy
http://www.heka.com/downloads/downloads_main.html#down_fitmaster
Software for analysis and fitting routines of electrophysiological data. Analysis can be performed on the levels of Sweeps/Traces and Series.
Proper citation: FITMASTER (RRID:SCR_016233) Copy
http://www.redshirtimaging.com/redshirt_neuro/software_aquisition.htm
Software for acquisition and analysis for imaging applications. The acquisition section has a variety of triggering and averaging modes, while the analysis section has extensive provisions for displaying traces (intensity vs time) and movies of propagating activity.
Proper citation: NeuroPlex (RRID:SCR_016193) Copy
https://fractalis.lcsb.uni.lu/
Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis.
Proper citation: Fractalis (RRID:SCR_016362) Copy
http://cole-trapnell-lab.github.io/monocle-release/docs/
Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.
Proper citation: Monocle2 (RRID:SCR_016339) Copy
https://github.com/KM-Lab/Electrographic-Seizure-Analyzer
Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.
Proper citation: Electrographic Seizure Analyzer (RRID:SCR_016344) Copy
https://amp.pharm.mssm.edu/biojupies/
Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text.
Proper citation: BioJupies (RRID:SCR_016346) Copy
https://bioconductor.org/packages/release/bioc/html/MAST.html
Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Proper citation: MAST (RRID:SCR_016340) Copy
https://www.ebi.ac.uk/metagenomics/
Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.
Proper citation: MGnify (RRID:SCR_016429) Copy
Python library for materials analysis codes. Defines core object representations for structures and molecules.
Proper citation: Pymatgen (RRID:SCR_016565) Copy
Software tool for assay data analysis.
Proper citation: MyAssays (RRID:SCR_016562) Copy
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