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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.
Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols.
Proper citation: Phenotypes and eXposures Toolkit (RRID:SCR_006532) Copy
FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain.
Proper citation: Flycircuit (RRID:SCR_006375) Copy
Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.
Proper citation: FlyBase (RRID:SCR_006549) Copy
https://github.com/Pithikos/C-Thread-Pool
Software for minimal but powerful thread pool in ANSI C.
Proper citation: C Thread Pool (RRID:SCR_023999) Copy
https://github.com/smirarab/sepp/
Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.
Proper citation: sepp (RRID:SCR_024327) Copy
https://www.teuniz.net/edflib/
Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files.
Proper citation: EDFlib (RRID:SCR_024010) Copy
http://www.dclunie.com/dicom3tools.html
Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files.
Proper citation: Dicom3tools (RRID:SCR_024008) Copy
https://github.com/stamatak/AxPcoords.dist
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets.
Proper citation: AxPcoords (RRID:SCR_023971) Copy
http://sco.h-its.org/exelixis/web/software/AxParafit/index.html
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets.
Proper citation: AxParafit (RRID:SCR_023968) Copy
https://github.com/nextstrain/auspice
Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data.
Proper citation: Auspice (RRID:SCR_023966) Copy
https://github.com/sanger-pathogens/assembly-stats
Software to get assembly statistics from FASTA and FASTQ files.
Proper citation: assembly-stats (RRID:SCR_023963) Copy
https://github.com/thegenemyers/DEXTRACTOR
Software as Bax file decoder and data compressor.
Proper citation: DEXTRACTOR (RRID:SCR_024005) Copy
https://github.com/nexml/nexml.java
Software repository contains java code for NeXML processing.
Proper citation: Java NeXML libraries and tools (RRID:SCR_024084) Copy
Web based integrative platform for transcriptional regulation studies.
Proper citation: Cistrome (RRID:SCR_000242) Copy
http://docking.sce.ntu.edu.sg/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor.
Proper citation: CovalentDock Cloud (RRID:SCR_000126) Copy
http://www.bioconductor.org/packages/release/bioc/html/cn.farms.html
Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff.
Proper citation: cn.FARMS (RRID:SCR_000289) Copy
Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data.
Proper citation: Dipy (RRID:SCR_000029) Copy
A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.
Proper citation: PyMOL (RRID:SCR_000305) Copy
http://www.ngsbicocca.org/html/fusion_analyser.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data.
Proper citation: Fusion Analyser (RRID:SCR_000059) Copy
http://bioconductor.org/packages/release/bioc/html/CorMut.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.
Proper citation: CorMut (RRID:SCR_000053) Copy
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