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https://github.com/SciCrunch/SciGraph

Software tool to represent ontologies and data described using ontologies as Neo4j graph. Ontology serving middleware tool using Neo4J as base server, able to ingest ttl files, and serve them to quickly create services that can underpin autocomplete, term lookup and tree traversal.

Proper citation: SciGraph (RRID:SCR_017576) Copy   

•   Source: SciCrunch Registry

https://crispy.secondarymetabolites.org

Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction.

Proper citation: CRISPy-web (RRID:SCR_017970) Copy   

•   Source: SciCrunch Registry

https://leora-software.com/products/poloplusonline

Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB.

Proper citation: PoloPlus USB Drive software (RRID:SCR_017614) Copy   

•   Source: SciCrunch Registry

http://statpackets.org/

Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together.

Proper citation: StatPackets (RRID:SCR_017613) Copy   

•   Source: SciCrunch Registry

https://kg.ebrains.eu/

Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems.

Proper citation: EBRAINS Knowledge Graph (RRID:SCR_017612) Copy   

•   Source: SciCrunch Registry

http://project-dare.eu/

EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously.

Proper citation: Project DARE (RRID:SCR_017538) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/wormlab

Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays.

Proper citation: Worm Lab (RRID:SCR_017669) Copy   

•   Source: SciCrunch Registry

https://scdevdb.deepomics.org/

Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes.

Proper citation: Single Cell Developmental Database (RRID:SCR_017546) Copy   

•   Source: SciCrunch Registry

https://github.com/LaBiOS/Transcriptive

Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results.

Proper citation: Transcriptive (RRID:SCR_017545) Copy   

•   Source: SciCrunch Registry

http://www.diploid.com/moon

Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid.

Proper citation: MOON (RRID:SCR_018005) Copy   

•   Source: SciCrunch Registry

http://paintmychromosomes.com/

Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data.

Proper citation: fineSTRUCTURE (RRID:SCR_018170) Copy   

•   Source: SciCrunch Registry

https://github.com/yousra291987/ChiCMaxima

Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling.

Proper citation: ChiCMaxima (RRID:SCR_018178) Copy   

•   Source: SciCrunch Registry

https://github.com/esctrionsit/snphub

Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.

Proper citation: SnpHub (RRID:SCR_018177) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SpydrPick

Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree.

Proper citation: SpydrPick (RRID:SCR_018176) Copy   

•   Source: SciCrunch Registry

http://www.innovision-systems.com/Products/MaxTraq.html

Software package for motion capture analysis by Innovision Systems Inc.

Proper citation: MaxTRAQ (RRID:SCR_018188) Copy   

•   Source: SciCrunch Registry

https://nemoanalytics.org/

Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.

Proper citation: NeMO Analytics (RRID:SCR_018164) Copy   

•   Source: SciCrunch Registry

https://github.com/WangHYLab/fcirc

Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs.

Proper citation: Fcirc (RRID:SCR_018090) Copy   

•   Source: SciCrunch Registry

https://dice-database.org

Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.

Proper citation: Database of Immune Cell Epigenomes (RRID:SCR_018259) Copy   

•   Source: SciCrunch Registry

https://github.com/AndreMacedo88/VEnCode

Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases.

Proper citation: VEnCode (RRID:SCR_018024) Copy   

•   Source: SciCrunch Registry

https://biit.cs.ut.ee/gprofiler/page/r

Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.

Proper citation: gProfiler2 (RRID:SCR_018190) Copy   

•   Source: SciCrunch Registry