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http://web.cmb.usc.edu/people/alber/Software/tomominer/

Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging.

Proper citation: TomoMiner (RRID:SCR_015045) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/madsim/index.html

A function which allows users to generate two biological conditions synthetic microarray datasets. The user provides a subset of parameters, but default parameter settings can be modified.

Proper citation: madsim (RRID:SCR_014765) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/papaya

A pure JavaScript medical research image viewer, compatible across a range of popular web browsers. The orthogonal viewer supports NIFTI and DICOM files, overlays and atlas labels. It requires Firefox (7+), Chrome (7+), Safari (6+), MobileSafari (iOS 6+), or IE (10+).

Proper citation: Papaya (RRID:SCR_014188) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/efficient_pt

A Matlab implementation for efficient permutation testing by using matrix completion.

Proper citation: Efficient Permutation Testing (RRID:SCR_014104) Copy   

•   Source: SciCrunch Registry

http://www.lji.org/faculty-research/scientific-cores/dlac/#overview

The department of laboratory animal care at the La Jolla Institute for Allergy and Immunology.

Proper citation: La Jolla Institute for Allergy and Immunology Department of Laboratory Animal Care (RRID:SCR_014834) Copy   

•   Source: SciCrunch Registry

http://dx.doi.org/10.5281/zenodo.21157

A graphical source code file used for an automated motion detection and reward system for animal training (see comment for full paper title). It was designed on the LabVIEW programming system. Running the program requires the appropriate LabVIEW runtime software from National Instruments Corporation.

Proper citation: Monkey Motion (RRID:SCR_014285) Copy   

•   Source: SciCrunch Registry

https://github.com/mateidavid/fast5

Software C++ library for accessing Oxford Nanopore Technologies sequencing data.

Proper citation: Fast5 Library (RRID:SCR_024023) Copy   

•   Source: SciCrunch Registry

https://github.com/TADA-A/TADA-A/tree/master

Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies.

Proper citation: TADA-A (RRID:SCR_024538) Copy   

•   Source: SciCrunch Registry

https://github.com/VioletteChiara/AnimalTA

Software video tracking tool for tracking and analysing animal movement in different environments.

Proper citation: AnimalTA (RRID:SCR_023784) Copy   

•   Source: SciCrunch Registry

https://biom-format.org/

Software provides command line interface and Python API for working with Biological Observation Matrix files.

Proper citation: python-biom-format (RRID:SCR_024193) Copy   

•   Source: SciCrunch Registry

https://github.com/opensafely-core

The code that runs the OpenSAFELY platform used for analysis of electronic health records data.

Proper citation: OpenSAFELY (RRID:SCR_023790) Copy   

•   Source: SciCrunch Registry

https://github.com/liqihang007/VIS_STEB

Web based visual analytics tool for the comprehensive exploration of genomic and phenotypic patterns, especially for the spatiotemporal patterns, in the developing mouse brain. The tool is designed in JavaScript and D3.js, the data is based on Allen Developing Mouse Brain Atlas (ADMBA) data.

Proper citation: Spatiotemporal pattern Exploration of Brain (RRID:SCR_023825) Copy   

•   Source: SciCrunch Registry

http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV/

Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins.

Proper citation: MetaPSICOV (RRID:SCR_024517) Copy   

•   Source: SciCrunch Registry

https://github.com/PapenfussLab/DMS_with_Alanine_scan

Code used for data processing, variant impact predictor modelling and result analysis. Used to improve prediction results to predict the impact of amino acid variants. Extended linear regression-based predictor to explore whether incorporating data from alanine scanning, widely-used low-throughput mutagenesis method, would improve prediction results.

Proper citation: DMS_with_Alanine_scan (RRID:SCR_023949) Copy   

•   Source: SciCrunch Registry

https://scikit-learn.org/stable/modules/generated/sklearn.svm.LinearSVC.html

Software application for linear support vector classification. Used in classification problems.

Proper citation: LinearSVC (RRID:SCR_024741) Copy   

•   Source: SciCrunch Registry

https://github.com/CahanLab/singleCellNet

Software tool to classify single cell RNA-Seq data across platforms and across species.

Proper citation: SingleCellNet (RRID:SCR_024742) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/org.Hs.eg.db/

Software R package as object for simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers.

Proper citation: org.Hs.eg.db (RRID:SCR_024739) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT

Software intra-modal motion correction tool designed for use on fMRI time series for linear (affine) inter- and inter-modal brain image registration.

Proper citation: MCFLIRT (RRID:SCR_024792) Copy   

•   Source: SciCrunch Registry

https://github.com/SlicerMorph/SlicerMorph

Open and extensible platform to retrieve, visualize and analyse 3D morphology.Extension to import microCT data and conduct 3D morphometrics in Slicer. Used for data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application.

Proper citation: SlicerMorph (RRID:SCR_024674) Copy   

•   Source: SciCrunch Registry

https://rpy2.github.io/

Software interface to use R from Python.

Proper citation: rpy2 (RRID:SCR_024701) Copy   

•   Source: SciCrunch Registry