Tools   Select Another Resource Report Type

http://hub.docker.com/r/marchalc/hicres/

Software pipeline to estimate and predict genomic resolution of Hi-C libraries. Used for estimating and predicting HiC library resolution.

Proper citation: HiCRes (RRID:SCR_022319) Copy   

•   Source: SciCrunch Registry

https://jump-cellpainting.broadinstitute.org

Consortium is creating new data driven approach to drug discovery based on cellular imaging, image analysis, and high dimensional data analytics. Creates public data set to validate and scale up this image based drug discovery strategy. By coordinating assay procedures across partners, future created data will be well matched. Aims to make cell images as computable as genomes and transcriptomes.

Proper citation: JUMP Cell Painting Consortium (RRID:SCR_021868) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/gernerlab/cytomap/-/wikis/home

Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information.

Proper citation: CytoMAP (RRID:SCR_021227) Copy   

•   Source: SciCrunch Registry

https://github.com/FRED-2/OptiType

Software tool for precision HLA typing from next generation sequencing data.

Proper citation: OptiType (RRID:SCR_022279) Copy   

•   Source: SciCrunch Registry

http://nf.synapse.org

Portal created to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis and schwannomatosis.Public data repository that stores and shares data generated by multiple collaborative research programs focused on neurofibromatosis diseases.

Proper citation: NF Data Portal (RRID:SCR_021683) Copy   

•   Source: SciCrunch Registry

https://github.com/B-UMMI/LMAS

Automated workflow enabling benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. Results are presented in interactive HTML report where selected global and reference specific performance metrics can be explored.

Proper citation: LMAS (RRID:SCR_022251) Copy   

•   Source: SciCrunch Registry

https://subcellular.humanbrainproject.eu/

Web interface for simulation of biological molecular networks. Web based environment for creation and simulation of reaction-diffusion models integrated with molecular repository. Allows to import, combine and simulate existing models expressed with BNGL and SBML languages. Application is integrated with number of solvers for reaction-diffusion systems of equations.

Proper citation: Subcellular App (RRID:SCR_018790) Copy   

•   Source: SciCrunch Registry

http://sanger-pathogens.github.io/snp-sites/

Software tool to find SNP sites from multi-FASTA alignment file. Can output results in multiple formats for downstream analysis.

Proper citation: SNP-sites (RRID:SCR_022265) Copy   

•   Source: SciCrunch Registry

https://github.com/dfguan/purge_dups

Software tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.

Proper citation: purge dups (RRID:SCR_021173) Copy   

•   Source: SciCrunch Registry

http://services.mbi.ucla.edu/anisoscale/

Web server to indicate severity of anisotropy in data set. Degree of anisotropy is indicated by anisotropic delta B statistic.

Proper citation: UCLA Diffraction Anisotropy Server (RRID:SCR_018722) Copy   

•   Source: SciCrunch Registry

https://pasquali-lab.gitlab.io/umi4cats/

Software R package for analyzing UMI-4C chromatin contact data. Used to analyze chromatin contact profiles obtained by UMI-4C.

Proper citation: UMI4Cats (RRID:SCR_021780) Copy   

•   Source: SciCrunch Registry

https://github.com/hahnlab/CAFExp

Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny.

Proper citation: Computational Analysis of gene Family Evolution (RRID:SCR_018924) Copy   

•   Source: SciCrunch Registry

http://mtshasta.phys.washington.edu/website/SuperSegger.php

Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells.

Proper citation: SuperSegger (RRID:SCR_018532) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/neuroethology-tools/

Software Python pipeline for automated detection, pose estimation, and behavior classification in socially interacting mice.Used for pose estimation and behavior quantification in pairs of freely behaving mice.

Proper citation: Mouse Action Recognition System (RRID:SCR_022347) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/alexmascension/triku

Software tool as feature selection method based on nearest neighbors for single-cell data.

Proper citation: triku (RRID:SCR_020977) Copy   

•   Source: SciCrunch Registry

https://github.com/lkmklsmn/DrivAER

Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data.

Proper citation: DrivAER (RRID:SCR_019076) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/autostereota/

Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control.

Proper citation: AutoStereota (RRID:SCR_022330) Copy   

•   Source: SciCrunch Registry

https://github.com/CEGRcode/stencil

Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise.

Proper citation: STENCIL (RRID:SCR_021878) Copy   

•   Source: SciCrunch Registry

https://gat.readthedocs.io/en/latest/

Software tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate.

Proper citation: Genomic Association Tester (RRID:SCR_020949) Copy   

•   Source: SciCrunch Registry

https://pm4ngs.readthedocs.io/

Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution.

Proper citation: PM4NGS (RRID:SCR_019164) Copy   

•   Source: SciCrunch Registry