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http://openmopac.net

Software program for semiempirical quantum chemistry for handling of biomolecules.

Proper citation: MOPAC (RRID:SCR_014898) Copy   

•   Source: SciCrunch Registry

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.microbesonline.org/fasttree/

Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution.

Proper citation: FastTree (RRID:SCR_015501) Copy   

•   Source: SciCrunch Registry

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

Source code for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. It was originally designed for processes observed at arbitrary times in continuous time but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.

Proper citation: MSM (RRID:SCR_015500) Copy   

•   Source: SciCrunch Registry

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

Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species.

Proper citation: phytools (RRID:SCR_015502) Copy   

•   Source: SciCrunch Registry

https://github.com/lucventurini/mikado/

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.

Proper citation: Mikado (RRID:SCR_016159) Copy   

•   Source: SciCrunch Registry

http://github.com/fraimondo/cudaica

Software that implements Infomax ICA, which is an algorithm to perform Independent Component Analysis, in CUDA (a parallel computing platform and programming model).

Proper citation: CUDAICA (RRID:SCR_015630) Copy   

•   Source: SciCrunch Registry

https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.. Regist custom genome software registers custom genomes to Genome Explorer (IN: FASTA).

Proper citation: regist custom genome (RRID:SCR_015999) Copy   

•   Source: SciCrunch Registry

https://github.com/Neuroinflab/kCSD-python

Source code for the Python implementation of the kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes.

Proper citation: kCSD-python (RRID:SCR_015777) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/lme4/index.html

Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue."

Proper citation: lme4 (RRID:SCR_015654) Copy   

•   Source: SciCrunch Registry

https://pythonvideoannotator.readthedocs.io/en/master/index.html

Software graphical application written in Python, to analyze videos and create notes for events in the video. Used to identify animals’ behaviors based on information extracted from video.

Proper citation: PythonVideoAnnotator (RRID:SCR_025868) Copy   

•   Source: SciCrunch Registry

https://github.com/mysql/mysql-server

Open source Relational Database Management System that enables users to store, manage, and retrieve structured data efficiently.

Proper citation: MySQL-server (RRID:SCR_025972) Copy   

•   Source: SciCrunch Registry

https://github.com/STAR-Fusion/STAR-Fusion

Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set.

Proper citation: STAR-Fusion (RRID:SCR_025853) Copy   

•   Source: SciCrunch Registry

https://www.php.net/

Popular general-purpose scripting language that is especially suited to web development.

Proper citation: PHP (RRID:SCR_025974) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=pracma

Software R package provides functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.

Proper citation: pracma (RRID:SCR_026021) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/methylSig.html

Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation.

Proper citation: MethylSig (RRID:SCR_025849) Copy   

•   Source: SciCrunch Registry

https://www.naaccr.org/

Professional organization that develops and promotes uniform data standards for cancer registration. Provides education and training, certifies population-based registries, aggregates and publishes data from central cancer registries and promotes the use of cancer surveillance data and systems for cancer control and epidemiologic research, public health programs, and patient care to reduce the burden of cancer in North America. Data Standards and Data Dictionary is intended for hospital and central cancer registries, programmers, and analysts. It provides detailed specifications and codes for each data item in the NAACCR data exchange record layout.

Proper citation: North American Association of Central Cancer Registries (RRID:SCR_026199) Copy   

•   Source: SciCrunch Registry

https://github.com/lens-biophotonics/ZetaStitcher

Software tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

Proper citation: ZetaStitcher (RRID:SCR_026193) Copy   

•   Source: SciCrunch Registry