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https://www.ebrains.eu/brain-atlases/analysis/gene-expression-analysis-in-human-brain-atlas-regions/

Software tool for integrating tissue transcriptome and cytoarchitectonic segregation. Combines data from Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, specifically to discover how gene activities and microanatomical architectures contribute to brain function and dysfunction. Both tissue transcriptome and probabilistic brain segregation data allow for integrating genetic expression, brain structure, and function knowledge.

Proper citation: JuGEx (RRID:SCR_023838) Copy   

•   Source: SciCrunch Registry

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

Software R package for query NCBI Entrez and retrieve PubMed records in XML or text format. Used to process PubMed records by extracting and aggregating data from selected fields. Large number of records can be downloaded via this simple-to-use interface to NCBI PubMed API. Used to search and retrieve scientific publication records from PubMed.

Proper citation: easyPubMed (RRID:SCR_023570) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/oligo.html

Software R package to analyze oligonucleotide arrays at probe level. Supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). Used for annotation of Affymetrix Gene Array data.

Proper citation: Preprocessing tools for oligonucleotide arrays (RRID:SCR_023726) Copy   

•   Source: SciCrunch Registry

https://github.com/petersaj/AP_histology

Software data pipeline which aligns histology images to the Allen CCF.

Proper citation: AP-histology (RRID:SCR_023847) Copy   

•   Source: SciCrunch Registry

http://www.listdiff.com/

Software tool that performs SET Operations including Set Intersections, Set Unions and Set Differences over lists of words, numbers etc with formatted results . Used for comparing differences between two lists.

Proper citation: ListDiff (RRID:SCR_023569) Copy   

•   Source: SciCrunch Registry

https://namsor.app/

Software tool accurately classifies personal names by gender, country of origin or ethnicity. Can infer gender, translate Chinese names and Japanese names, format phone number, and split full name via user interface and API. Used as name checker for gender, origin and ethnicity determination.

Proper citation: NamSor (RRID:SCR_023935) Copy   

•   Source: SciCrunch Registry

https://github.com/AstraZeneca-NGS/VarDictJava

Software tool as variant caller for both single and paired sample variant calling from BAM files. Implements amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads.Novel and versatile variant caller for next generation sequencing in cancer research.

Proper citation: VarDict (RRID:SCR_023658) Copy   

•   Source: SciCrunch Registry

https://app.grammarly.com/

Software to correct spelling and grammar.

Proper citation: Grammarly (RRID:SCR_023778) Copy   

•   Source: SciCrunch Registry

https://www.chemcomp.com/Products.htm

Drug discovery platform to integrate visualization, modeling and simulation in single package. Integrated computer aided molecular design platform.

Proper citation: Molecular Operating Environment (RRID:SCR_023932) Copy   

•   Source: SciCrunch Registry

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