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https://github.com/biocatiit/musclex

Software suite as collection of programs intended to assist with analyzing diffraction X-ray images. MuscleX diffraction X-ray image analyzing toolkit. Data reduction software for X-ray fiber diffraction data.

Proper citation: Muscle X (RRID:SCR_018811) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Trinotate/Trinotate.github.io/wiki

Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

Proper citation: Trinotate (RRID:SCR_018930) Copy   

•   Source: SciCrunch Registry
  

http://webapps.embl-hamburg.de/rapido/

Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains.

Proper citation: RAPIDO (RRID:SCR_018935) Copy   

•   Source: SciCrunch Registry
  

http://xena.ucsc.edu/

Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables.

Proper citation: UCSC Xena (RRID:SCR_018938) Copy   

•   Source: SciCrunch Registry
  

https://www.siemens-healthineers.com/en-us/angio/options-and-upgrades/clinical-software-applications/syngo-dynact

Software tool to construct 3D models of soft tissue using CT-like cross sectional imaging.

Proper citation: syngo DynaCT (RRID:SCR_018902) Copy   

•   Source: SciCrunch Registry
  

http://rats.pub

Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords.

Proper citation: RatsPub (RRID:SCR_018905) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/abcdrepronim/

Course provides training for reproducible analyses of Adolescent Brain Cognitive Development Study data. Designed to provide comprehensive background to ABCD study while delivering hands on instruction on reproducible ReproNim workflows and outcomes.

Proper citation: ABCD-ReproNim Course (RRID:SCR_018911) Copy   

•   Source: SciCrunch Registry
  

https://nanopore.usegalaxy.eu/

Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.

Proper citation: NanoGalaxy (RRID:SCR_018912) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/scTHI/

Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.

Proper citation: scTHI (RRID:SCR_018918) Copy   

•   Source: SciCrunch Registry
  

https://www.t2dsystems.eu/t2dsystems

Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D.

Proper citation: T2DSystems (RRID:SCR_018913) Copy   

•   Source: SciCrunch Registry
  

http://diabeticfootconsortium.org/

Group of academic institutions committed to studying diabetic foot conditions, such as foot ulcers and wound healing, to develop predictive biomarkers which can be later used to create better treatment plans and improve health and quality of life for people living with diabetes.

Proper citation: Diabetic Foot Consortium (RRID:SCR_018914) Copy   

•   Source: SciCrunch Registry
  

https://www.leicabiosystems.com/histology-equipment/tissue-processors/products/leica-asp300-s/

Processor that automatically washes tissue sample which needs to be usable in downstream processes. Designed for routine and research histopathology of up to 300 cassettes.

Proper citation: Leica: ASP300S Fully Enclosed Tissue Processor (RRID:SCR_018916) Copy   

•   Source: SciCrunch Registry
  

https://mcule.com/

Software drug discovery platform to integrate purchasable chemical space with molecular modeling tools. Chemical marketplace for drug discovery with services based around small molecule compound sourcing. Integrated molecular modeling tools, compound database, IT infrastructure and compound procurement service with web interface. Virtual screens can be run to identify new hits and modeling applications can be used to improve their affinity and other properties.

Proper citation: Mcule (RRID:SCR_018921) Copy   

•   Source: SciCrunch Registry
  

https://github.com/najasplus/hetindel_shinyapp

Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.

Proper citation: Hetindel (RRID:SCR_018922) Copy   

•   Source: SciCrunch Registry
  

http://www.nonlinear.com/progenesis/qi-for-proteomics/

Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics.

Proper citation: Progenesis QI (RRID:SCR_018923) Copy   

•   Source: SciCrunch Registry
  

http://www.cgga.org.cn/

Web application for data storage and analysis to explore brain tumors datasets from Chinese cohorts. Data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes primary and recurrent glioma samples from Chinese cohorts. Allows users to browse DNA mutation profile, mRNA/microRNA expression profile and methylation profile, and to do correlation and survival analysis in specific glioma subtype.

Proper citation: Chinese Glioma Genome Atlas (RRID:SCR_018802) Copy   

•   Source: SciCrunch Registry
  

https://github.com/davidebolo1993/TRiCoLOR

Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments.

Proper citation: TRiCoLOR (RRID:SCR_018801) Copy   

•   Source: SciCrunch Registry
  

https://www.agilent.com/en/product/liquid-chromatography/hplc-systems/application-specific-hplc-systems/1290-infinity-ii-online-spe-system

Online SPE System automates solid phase extraction to enrich analytes, remove matrix components or lower detection limits.

Proper citation: Agilent: 1290 Infinity II Online SPE System (RRID:SCR_019380) Copy   

•   Source: SciCrunch Registry
  

https://www.otago.ac.nz/chatterjee-lab/tools/index.html

Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity.

Proper citation: Differential Methylation Analysis Package (RRID:SCR_019148) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Griffan/FASTQuick

Software tool for rapid and comprehensive quality assessment of raw sequence reads. It generates comprehensive list of QC statistics, including ancestry and contamination estimation.

Proper citation: FASTQuick (RRID:SCR_019269) Copy   

•   Source: SciCrunch Registry