Tools   Select Another Resource Report Type

https://hdmf.readthedocs.io/

Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data.

Proper citation: Hierarchical Data Modeling Framework (RRID:SCR_021303) Copy   

•   Source: SciCrunch Registry

https://cometbio.org/

Software tool to quantify comet parameters while studying DNA strand breaks. Automated tool for comet assay image analysis.

Proper citation: OpenComet (RRID:SCR_021826) Copy   

•   Source: SciCrunch Registry

https://www.fredhutch.org/en/research/shared-resources.html

Through Shared Resources, investigators in Fred Hutch/University of Washington Cancer Consortium and external academic and industry organizations can access services tailored to their specific research goals, including novel assay development or early access to new technologies.

Proper citation: Fred Hutchinson Cancer Center Shared Resources (RRID:SCR_022607) Copy   

•   Source: SciCrunch Registry

https://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html

Software library that exports C++ mmCIF accessors to Python.

Proper citation: Core Wrapper (RRID:SCR_024087) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/cyvcf2

Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis.

Proper citation: cyvcf2 (RRID:SCR_024000) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/nanolyse

Software package to remove reads mapping to the lambda phage genome from a fastq file.

Proper citation: NanoLyse (RRID:SCR_024125) Copy   

•   Source: SciCrunch Registry

https://www.utsouthwestern.edu/labs/danuser/software/

Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences.

Proper citation: plusTipTracker (RRID:SCR_021890) Copy   

•   Source: SciCrunch Registry

https://github.com/NeLy-EPFL/DeepFly3D

Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose.

Proper citation: DeepFly3D (RRID:SCR_021402) Copy   

•   Source: SciCrunch Registry

https://simpleitk.org/

Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms.

Proper citation: SimpleITK (RRID:SCR_024693) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/gwBrowser/

An interactive web application for visualizing genomic data of sequenced prokaryotic chromosomes. It allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences.

Proper citation: GeneWiz browser (RRID:SCR_001454) Copy   

•   Source: SciCrunch Registry

https://github.com/khowe/quicktree/

Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments.

Proper citation: quicktree (RRID:SCR_024205) Copy   

•   Source: SciCrunch Registry

https://github.com/SciTools/cartopy

Software Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses. Cartographic library with matplotlib support.

Proper citation: Cartopy (RRID:SCR_024587) Copy   

•   Source: SciCrunch Registry

https://mc-stan.org/bayesplot/

Software R package providing extensive library of plotting functions for use after fitting Bayesian models.Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow.

Proper citation: bayesplot (RRID:SCR_024588) Copy   

•   Source: SciCrunch Registry

https://pyepl.sourceforge.net/

Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses.

Proper citation: pyepl (RRID:SCR_024182) Copy   

•   Source: SciCrunch Registry

https://harvest.readthedocs.io/en/latest/content/parsnp.html

Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

Proper citation: Parsnp (RRID:SCR_024153) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html

Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.

Proper citation: PDB2PQR (RRID:SCR_024155) Copy   

•   Source: SciCrunch Registry

https://github.com/sib-swiss/pftools3

Software suite of tools to build and search generalized profiles.

Proper citation: PfTools (RRID:SCR_024158) Copy   

•   Source: SciCrunch Registry

https://jydu.github.io/physamp/

Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.

Proper citation: PhySamp (RRID:SCR_024159) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/bxlab/bx-python

Software Python library and associated set of scripts for rapid implementation of genome scale analyses.

Proper citation: python-bx (RRID:SCR_024202) Copy   

•   Source: SciCrunch Registry