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https://chat.openai.com/

Artificial Iinteligence chatbot that uses natural language processing to create humanlike conversational dialogue. Notable for enabling users to refine and steer conversation towards desired length, format, style, level of detail, and language used. Sibling model to InstructGPT, which is trained to follow instruction in prompt and provide detailed response.

Proper citation: ChatGPT (RRID:SCR_023775) Copy   

•   Source: SciCrunch Registry

https://github.com/singleron-RD/CeleScope

Software tool as collection of bioinfomatics analysis pipelines to process single cell sequencing data generated with Singleron products. Single cell analysis pipelines developed by Singleron Biotechnologies.

Proper citation: CeleScope (RRID:SCR_023553) Copy   

•   Source: SciCrunch Registry

https://github.com/SainsburyWellcomeCentre/ara_tools

Software package for analysis of mouse brain STP data with respect to the Allen Reference Atlas. Collection of MATLAB functions to analyze mouse whole brain imaging data and the associated "sparse" point data such as cell locations, traced neurite trees, or traced projections from a bulk injection. This package relates sparse data to the Allen Mouse Brain Reference Atlas.

Proper citation: ARA Tools (RRID:SCR_023826) Copy   

•   Source: SciCrunch Registry

http://virusdetect.feilab.net/cgi-bin/virusdetect/index.cgi

Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs.

Proper citation: VirusDetect (RRID:SCR_023669) Copy   

•   Source: SciCrunch Registry

https://github.com/GuillermoPoblete/PGL

Software R package which links genetics and human brain imaging by using genes associated with disease and calculating normalized mRNA expression average of those genes in each brain region. By uploading lists of genes and brain regions of interest, this package will return csv with the results.

Proper citation: Process Genes List (RRID:SCR_023823) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/spm_mouse_toolb#

Software toolbox provides multi-modality murine image templates, all of which are spatially registered to the Allen Common Coordinate Framework. The images have been optimized for in-vivo preclinical imaging in terms of resolution and region-of-interest size. The ROIs have been derived from the Allen Brain Atlas. This image analysis tool can be used to facilitate the analysis of mouse PET-CT brain images.

Proper citation: PET-CT mouse brain toolbox (RRID:SCR_023821) Copy   

•   Source: SciCrunch Registry

https://github.com/churchmanlab/genewalk

Software for individual genes functions determination that are relevant in particular biological context and experimental condition. Quantifies similarity between vector representations of gene and annotated GO terms through representation learning with random walks on condition specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks.

Proper citation: GeneWalk (RRID:SCR_023787) Copy   

•   Source: SciCrunch Registry

https://github.com/biod/sambamba

Software tool to filter SAM file for soft and hard clipped alignments

Proper citation: samclip (RRID:SCR_024330) Copy   

•   Source: SciCrunch Registry

https://github.com/ekg/seqwish

Software tool for alignment to variation graph inducer.

Proper citation: seqwish (RRID:SCR_024332) Copy   

•   Source: SciCrunch Registry

https://github.com/cbrnr/sigviewer

Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections.

Proper citation: sigviewer (RRID:SCR_024340) Copy   

•   Source: SciCrunch Registry

http://www.pyomo.org/

Open source Python-based optimization modeling language with diverse set of optimization capabilities.

Proper citation: pyomo (RRID:SCR_024188) Copy   

•   Source: SciCrunch Registry

http://sitplus.crea-si.com/index/index.html

Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities.

Proper citation: sitplus (RRID:SCR_024344) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/AI-FANN

Software Perl wrapper for the Fast Artificial Neural Network library

Proper citation: AI-FANN (RRID:SCR_024060) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Coordinate

Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.

Proper citation: Bio-Coordinate (RRID:SCR_024063) Copy   

•   Source: SciCrunch Registry

https://www.artinis.com/oxysoft

Software application used to collect, store, view, and analyse all necessary data from the Brite Family devices, PortaMon, PortaLite, OctaMon and OxyMon developed by Artinis Medical Systems and highly customisable to individual requirements.

Proper citation: Artinis Medical Systems Oxysoft (RRID:SCR_024666) Copy   

•   Source: SciCrunch Registry

https://lifesciences.tecan.com/plate_readers/infinite_200_pro?p=tab--3

Microplate reader software as user friendly interface for control of Tecan's Infinite series of microplate readers designed for professional use.

Proper citation: Tecan i-Control (RRID:SCR_024562) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/StereoCell_v2.0

Enhanced application on generating single cell gene expression profile for high resolution spatial transcriptomics. Registers spatial gene expression map and cell membrane/wall staining image with nuclei staining image as intermediary, thus cell membrane/wall outlines can be directly segmented from cell membrane/wall staining image without correcting nuclei boundaries.

Proper citation: StereoCell v2.0 (RRID:SCR_024438) Copy   

•   Source: SciCrunch Registry

https://github.com/kblin/ncbi-acc-download

Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.

Proper citation: NCBI accession download script (RRID:SCR_024130) Copy   

•   Source: SciCrunch Registry

https://lucy.sourceforge.net/

Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses.

Proper citation: Lucy (RRID:SCR_024099) Copy   

•   Source: SciCrunch Registry

http://tacg.sourceforge.net/

Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA.

Proper citation: tacg (RRID:SCR_024374) Copy   

•   Source: SciCrunch Registry