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https://github.com/PedroMTQ/mantis

Software homology based protein function annotation tool that integrates multiple reference data sources. Custom reference data sources can also be added.Accepts as input aminoacids sequence fasta. Customizable and is available on Linux.

Proper citation: Mantis (RRID:SCR_021001) Copy   

•   Source: SciCrunch Registry

https://pypi.org/

Software repository for Python programming language.Used to find and install software developed and shared by Python community.

Proper citation: PyPI (RRID:SCR_023145) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/FilterFFPE/

Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.

Proper citation: FilterFFPE (RRID:SCR_021086) Copy   

•   Source: SciCrunch Registry

https://www.bioinformatics.nl/cgi-bin/emboss/getorf

Web application to find and extract open reading frames (ORFs). Used to find and output sequences of open reading frames in one or more nucleotide sequences.

Proper citation: getorf (RRID:SCR_024691) Copy   

•   Source: SciCrunch Registry

https://www.photometrics.com/products/ocular

Photometrics acquisition software to capture, save and publish images and movies. Allows users of color and monochrome cameras to capture high quality images and videos from their microscope or lens system.

Proper citation: Ocular (RRID:SCR_024467) Copy   

•   Source: SciCrunch Registry

https://github.com/qiyueyang-7/scNTImpute.git

Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data.

Proper citation: scNTImpute (RRID:SCR_024395) Copy   

•   Source: SciCrunch Registry

https://github.com/GreenleafLab/ChrAccR

Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets.

Proper citation: ChrAccR (RRID:SCR_024397) Copy   

•   Source: SciCrunch Registry

https://portal.brain-map.org/atlases-and-data/bkp/mapmycells

MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells.

Proper citation: MapMyCells (RRID:SCR_024672) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/EAGS

Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell.

Proper citation: Efficient and Adaptive Gaussian Smoothing (RRID:SCR_024399) Copy   

•   Source: SciCrunch Registry

https://www.olympus-lifescience.com/en/downloads/detail-iframe/?0[downloads][id]=847249651

Software for image processing. Reads data captured by FV1200/FV1000/FV500/FV300 microscopes. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read.

Proper citation: Olympus FV10-ASW Viewer (RRID:SCR_024433) Copy   

•   Source: SciCrunch Registry

http://mpds.neist.res.in:8085/

Galaxy based disease specific web portal for drug discovery research of COVID-19. Open access disease specific drug discovery portal.

Proper citation: Molecular Property Diagnostic Suite Covid-19 (RRID:SCR_024545) Copy   

•   Source: SciCrunch Registry

https://prosite.expasy.org/scanprosite/

Web tool for detecting PROSITE signature matches in protein sequences.

Proper citation: ScanProsite (RRID:SCR_024425) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/BatchEval

Software tool for evaluating batch effects in data integration. Tool to improve accuracy and reliability of experimental results. Used to evaluate batch effect of dataset integration and output comprehensive report.

Proper citation: BatchEval (RRID:SCR_024546) Copy   

•   Source: SciCrunch Registry

https://science.bostongene.com/kassandra/

Software bulk RNA-seq cellular deconvolution tool. Used for analysis of healthy tissue and tumor biopsies. Based on RNA-seq NGS data of biological sample, Kassandra predicts cellular composition including stromal and immune elements by analyzing gene expression.

Proper citation: Kassandra (RRID:SCR_024548) Copy   

•   Source: SciCrunch Registry

https://github.com/cchandre/Polarimetry

Software Python based app for analyzing polarization resolved microscopy data to measure molecular orientation and order in biological samples.

Proper citation: PyPOLAR (RRID:SCR_024681) Copy   

•   Source: SciCrunch Registry

https://github.com/katiasmirn/PERFect#perfect-permutation-filtering-package-in-r

Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering.

Proper citation: PERFect (RRID:SCR_024682) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/DrugSim2DR/

Software R package to predict drug functional similarity to drug repurposing.

Proper citation: DrugSim2DR (RRID:SCR_024564) Copy   

•   Source: SciCrunch Registry

https://seer.cancer.gov/csr/1975_2016/

Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States.

Proper citation: NCI SEER Cancer Statistics Review (RRID:SCR_024685) Copy   

•   Source: SciCrunch Registry

https://ganjoho.jp/public/index.html

Portal provides information on Cancer Statistics in Japan. Official website operated by National Cancer Center for cancer information.

Proper citation: Cancer Information Service (RRID:SCR_024445) Copy   

•   Source: SciCrunch Registry

https://www.sfwmd.gov/our-work/cerp-project-planning

Platform provides framework for restoring, protecting and preserving the greater Everglades ecosystem. The plan is partnership between State of Florida and federal government.

Proper citation: Comprehensive Everglades Restoration Plan (RRID:SCR_024557) Copy   

•   Source: SciCrunch Registry