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https://bioconductor.org/packages/ChIPseeker/

Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Proper citation: ChIPseeker (RRID:SCR_021322) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/calN50/

Software tool as simple script to calculate N50/NG50 and auN/auNG.

Proper citation: calN50 (RRID:SCR_022015) Copy   

•   Source: SciCrunch Registry

https://github.com/chenxinfeng4/ArControl

Software tool as Arduino UNO/Mega based, visual programming and real-time behavioral platform for neuroscience. It can run Go/No-Go, 2AFPC and Optogenetic stimulation tasks. Stand alone and intuitive Gaphical User Interface application.Part of ArControl system.

Proper citation: ArControl (RRID:SCR_021605) Copy   

•   Source: SciCrunch Registry

https://gbrs.readthedocs.io/en/latest/

Software suite of tools for reconstructing genomes using RNA-Seq data from multiparent population and for quantifying allele specific expression.

Proper citation: GBRS (RRID:SCR_020963) Copy   

•   Source: SciCrunch Registry

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

Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

Proper citation: survival (RRID:SCR_021137) Copy   

•   Source: SciCrunch Registry

https://pysam.readthedocs.io/en/latest/api.html

Software tool as interface for reading and writing SAM files. Python module to read and manipulate mapped short read sequence data stored in SAM/BAM files. Lightweight wrapper of htslib C-API.

Proper citation: pysam (RRID:SCR_021017) Copy   

•   Source: SciCrunch Registry

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

Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.

Proper citation: caret (RRID:SCR_021138) Copy   

•   Source: SciCrunch Registry

https://github.com/bonvision

Open source software package for creating and controlling visual environments.Software package for Bonsai which allows for control of 2D and 3D environments.

Proper citation: BonVision (RRID:SCR_021534) Copy   

•   Source: SciCrunch Registry

https://github.com/VisionandCognition/Tracker-MRI

Software package for experimental control from Vision and Cognition Lab at Netherlands Institute for Neuroscience. Matlab based software for fMRI, Psychophysical experimentation and NHP training, with eye control using Measurement and Computing IO card. Interfaces with ISCAN eye tracker and communicates with the MRI console using trigger pulses. Uses Psychtoolbox3 graphics and control engine.

Proper citation: Tracker MRI (RRID:SCR_021816) Copy   

•   Source: SciCrunch Registry

https://github.com/ISA-tools/isa-api

Open platform for interoperable life science experimental metadata. Metadata framework as set of community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in life sciences. Python library for creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats.Provides programmatic metadata handling functionality to support automation, common interface and interoperable medium between two ISA formats, as well as with other life science data formats required for depositing data in public databases.

Proper citation: ISA API (RRID:SCR_020980) Copy   

•   Source: SciCrunch Registry

https://github.com/cosanlab/facesync

Open source software Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.Framework for recording facial expressions with head mounted cameras.

Proper citation: FaceSync (RRID:SCR_021396) Copy   

•   Source: SciCrunch Registry

https://github.com/UmSenhorQualquer/d-track/blob/master/docs/source/index.rst

Software package to track object in 3D based on 3D schematics of scene.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins.

Proper citation: D-Track (RRID:SCR_021394) Copy   

•   Source: SciCrunch Registry

https://www.7-zip.org

Open source software tool as file archiver with high compression ratio.

Proper citation: 7-Zip (RRID:SCR_021270) Copy   

•   Source: SciCrunch Registry

https://github.com/DeepLabCut/DeepLabCut

Open source software package for markerless pose estimation. 2D keypoint detection in animals.

Proper citation: DeepLabCut (RRID:SCR_021391) Copy   

•   Source: SciCrunch Registry

https://github.com/ModelOriented/randomForestExplainer

Software R package to help explain which variables are most important in random forests. Various variable importance measures are calculated and visualized in different settings in order to get idea on how their importance changes classification or regression model accuracy.

Proper citation: randomForestExplainer (RRID:SCR_021823) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/karyoploteR/

Software R package used to karyoplots. Bioconductor package to plot customizable genomes displaying arbitrary data.

Proper citation: karyoploteR (RRID:SCR_021824) Copy   

•   Source: SciCrunch Registry

https://github.com/sqjin/CellChat

Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.

Proper citation: CellChat (RRID:SCR_021946) Copy   

•   Source: SciCrunch Registry

https://github.com/PedroMTQ/mantis

Software homology based protein function annotation tool that integrates multiple reference data sources. Custom reference data sources can also be added.Accepts as input aminoacids sequence fasta. Customizable and is available on Linux.

Proper citation: Mantis (RRID:SCR_021001) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/pyani/

Software package and script for calculation of genome scale average nucleotide identity. Python3 module that provides support for calculating average nucleotide identity and related measures for whole genome comparisons, and rendering relevant graphical summary output. Where available, it takes advantage of multicore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.

Proper citation: Pyani (RRID:SCR_021088) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/FilterFFPE/

Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.

Proper citation: FilterFFPE (RRID:SCR_021086) Copy   

•   Source: SciCrunch Registry