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http://sccn.ucsd.edu/wiki/BCILAB

Open Source MATLAB toolbox and EEGLAB plugin for the design, prototyping, testing, experimentation with, and evaluation of Brain-Computer Interfaces (BCIs), and other systems in the same computational framework. It facilitates the design and development of new methods for cognitive state estimation and their use in both offline data analysis and real-time applications. BCILAB includes an easily extensible collection of currently over 100 methods from the literature (covering signal processing, machine learning and BCI-specific methods). Aside from supporting advanced BCI research, a special aim of BCILAB is to facilitate the adoption of machine learning and advanced statistical modeling for functional neuroimaging purposes in tandem with the EEGLAB platform. The toolbox offers multiple different interfaces which link to the same backend functionality, including a GUI, scripting support (MATLAB-based), APIs for real-time processing, and a variety of extension component interfaces. MATLAB programming is not strictly necessary, as most BCILAB features can be accessed from the GUI, although it is required for batch scripting and custom extensions. The strength of MATLAB-based software lies in its resources for leading-edge scientific computing, as well as in the good support for rapid prototyping, but BCI systems developed in it can be used for real-time out-of-lab experimentation, and can in principle be deployed without the need for a MATLAB license. However, due to the complexity and overhead of the MATLAB environment, the system is best used as a research platform, and not as a product development environment -- end-user software is ideally re-implemented in a compiled language, after a suitable approach has been identified and extensively tested. The process of identifying and testing an approach involves more than just computation, but also data exploration and investigation - an area which is helped by the deep integration with the EEGLAB platform. In the future, this integration will be further strengthened, bringing rich statistical learning and signal processing into routine EEG analysis workflows. The toolbox has been developed by C. Kothe at the Swartz Center, inspired by the preceding PhyPA BCI toolbox created by C. Kothe and T. Zander at the Chair for Human-Machine Systems, Berlin Institute of Technology.

Proper citation: BCILAB (RRID:SCR_007013) Copy   

•   Source: SciCrunch Registry

https://github.com/Illumina/strelka/

Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller.

Proper citation: Strelka2 (RRID:SCR_005109) Copy   

•   Source: SciCrunch Registry

https://github.com/a-ludi/dentist

Software as automated pipeline method to close gaps in assemblies with long reads. Used to close assembly gaps using long reads at high accuracy.

Proper citation: DENTIST (RRID:SCR_021856) Copy   

•   Source: SciCrunch Registry

https://imbalanced-learn.org/stable/

Software Python package to tackle curse of imbalanced datasets in machine learning.Offers number of re-sampling techniques commonly used in datasets showing strong between class imbalance.

Proper citation: imblearn (RRID:SCR_021698) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/peppy/

Software python package for reading Portable Encapsulated Projects or PEPs in python.

Proper citation: peppy (RRID:SCR_021078) Copy   

•   Source: SciCrunch Registry

https://github.com/zhuangjun1981/corticalmapping

Software package for basic visual stimulation, imaging analysis, plotting, and cell visual response properties analysis functionality for calcium imaging.

Proper citation: corticalmapping (RRID:SCR_021871) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/eido/

Software validation tool for Portable Encapsulated Projects or PEPs in python.

Proper citation: eido (RRID:SCR_021076) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=CCP

Software R package for significance tests for canonical correlation analysis, including asymptotic tests and Monte Carlo method.

Proper citation: CCP (RRID:SCR_021745) Copy   

•   Source: SciCrunch Registry

https://github.com/portugueslab/stytra

Open source software Python package to control stimulation and track behaviour.Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations.

Proper citation: Stytra (RRID:SCR_021500) Copy   

•   Source: SciCrunch Registry

https://github.com/openworm/tracker-commons

Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis.

Proper citation: Worm Behavior Platform (RRID:SCR_021501) Copy   

•   Source: SciCrunch Registry

https://usegalaxy.eu

Software tools for analysis of data independent acqusition type proteomics data are implemented in Galaxy framework. Enables complete DIA data analysis including spectral library generation based on DDA type data, analysis of DIA data in raw or mzml format, and differntial statistical analysis. All tools are based on open-source software such as diypasef, OpenSwath, swath2stats and MSstats.

Proper citation: Data independent acquisition proteomics workbench (RRID:SCR_021862) Copy   

•   Source: SciCrunch Registry

https://github.com/zeyang-shen/maggie

Software Python package for identifying motifs mediating transcription factor binding and function. Links mutations of motif to changes of epigenomic feature without assuming linear relationship.

Proper citation: Motif Alteration Genome wide to Globally Investigate Elements (RRID:SCR_021903) Copy   

•   Source: SciCrunch Registry

https://github.com/bi-compbio/scrnax/

Software pipeline to improve gene annotation for cross species analysis of single cell RNA-Seq. Cross-species transfer of high quality 3’UTR annotation for single cell RNA-Seq.

Proper citation: scRNAx (RRID:SCR_022091) Copy   

•   Source: SciCrunch Registry

https://github.com/gatech-genemark/ProtHint

Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences.

Proper citation: ProtHint (RRID:SCR_021167) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/r8s/

Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies.

Proper citation: r8s (RRID:SCR_021161) Copy   

•   Source: SciCrunch Registry

https://github.com/KULL-Centre/BME

Software Python package to construct conformational ensemble of biomolecular system by integrating molecular simulations and experimental data. Performs ensemble reweighting using Bayesian Maximum Entropy approach.

Proper citation: BME (RRID:SCR_021953) Copy   

•   Source: SciCrunch Registry

https://artistoo.net

Software toolbox, formerly called CPMjs, as framework to build interactive, explorable simulation models of cells and tissues in web browser. JavaScript library to build interactive Cellular Potts Models as command line applications or in web browser.

Proper citation: Artistoo (RRID:SCR_020983) Copy   

•   Source: SciCrunch Registry

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

Software R package to Fit Bayesian stochastic block models and multi level stochastic block models using efficient Gibbs sampling implemented in Rcpp. Models assume symmetric, non reflexive graphs with unweighted, binary edges. Data are input as symmetric binary adjacency matrix, or list of such matrices.

Proper citation: MLSBM (RRID:SCR_021795) Copy   

•   Source: SciCrunch Registry

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

Software R package creating customizable presentation ready tables, summarizing data sets, regression models, and more. Used for publication ready data summary and analytic result tables.

Proper citation: gtsummary (RRID:SCR_021319) Copy   

•   Source: SciCrunch Registry

https://github.com/yhoogstrate/bam-lorenz-coverage

Software package to generate Lorenz plots and Coverage plots, directly from BAM file. It can also output tables as text documents so you can generate custom plots. There is also support to only analyse specific regions.

Proper citation: bam-lorenz-coverage (RRID:SCR_021837) Copy   

•   Source: SciCrunch Registry