Tools   Select Another Resource Report Type

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://pypi.org/project/findmaxima2d/

Software Python 2D Maxima finding algorithm. Re-implementation of Java plugin for ImageJ/Fiji.

Proper citation: findmaxima2d (RRID:SCR_023332) 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://www.dtu.ox.ac.uk/homacalculator/

Software tool used to calculate Homeostasis Model Assessment which takes account of variations in hepatic and peripheral glucose resistance, increases in insulin secretion curve for plasma glucose concentrations and contribution of circulating proinsulin. Provides access to HOMA2 model for researchers who wish to use model derived estimates of %B and %S, rather than linear approximations.

Proper citation: HOMA2 calculator (RRID:SCR_023419) Copy   

•   Source: SciCrunch Registry

https://www.vitalimages.com/enterprise-imaging-solution/diagnostic-viewer/

Software application providing tools and features that may be used for general purpose radiological viewing and reading of image data from various imaging modalities, clinical review and performs functions of digital image processing, measurement, communications and storage.

Proper citation: Vitrea Read Diagnostic Viewer (RRID:SCR_023418) 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://bioconductor.org/packages/release/bioc/html/panelcn.mops.html

Software R package as CNV detection tool for targeted NGS panel data. Extension of cn.mops package. Used for detecting copy number variations in targeted next generation sequencing panel data. Suitable to use for clinical geneticists for routine clinical diagnostics.

Proper citation: panelcn.mops (RRID:SCR_023657) 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/lufuhao/mitochondria-simulator

Software repository for mtDNA assembly project.

Proper citation: mitochondria simulator (RRID:SCR_023430) Copy   

•   Source: SciCrunch Registry

https://github.com/mgharvey/misc_python/blob/master/bin/TreeMix/treemix_tree_with_bootstraps.py

Phython script for bootstraping Treemix snp trees to generate confidance intervals in the main tree.

Proper citation: treemix_tree_with_bootstraps.py (RRID:SCR_023426) 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/miRTop/mirtop

Command lines tool to annotate miRNAs with standard mirna/isomir naming.

Proper citation: mirtop (RRID:SCR_024116) Copy   

•   Source: SciCrunch Registry

http://www-igm.univ-mlv.fr/~marsan/smile_english.html

Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.

Proper citation: SMILE (RRID:SCR_024119) 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