Tools   Select Another Resource Report Type

https://www.crisprscan.org/

Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR.

Proper citation: CRISPRscan (RRID:SCR_023777) Copy   

•   Source: SciCrunch Registry

https://www.cancermodels.org/

Cancer research platform that aggregates clinical, genomic and functional data from various types of patient derived cancer models, xenographs, organoids and cell lines. Open catalog of harmonised patient-derived cancer models. Standardises, harmonises and integrates clinical metadata, molecular and treatment-based data from academic and commercial providers worldwide. Data is FAIR and underpins generation and testing of new hypotheses in cancer mechanisms and personalised medicine development. PDCM Finder have expanded to organoids and cell lines and is now called CancerModels.Org. PDCM Finder was launched in April 2022 as successor of PDX Finder portal, which focused solely on patient-derived xenograft models.

Proper citation: CancerModels.Org (RRID:SCR_023931) Copy   

•   Source: SciCrunch Registry

https://pmc.ncbi.nlm.nih.gov/articles/PMC4525701/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products.

Proper citation: Poly Peak Parser (RRID:SCR_023776) Copy   

•   Source: SciCrunch Registry

https://jydu.github.io/maffilter/

Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.

Proper citation: MafFilter (RRID:SCR_024105) Copy   

•   Source: SciCrunch Registry

https://github.com/Pas-Kapli/mptp

Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets.

Proper citation: mPTP (RRID:SCR_024121) Copy   

•   Source: SciCrunch Registry

http://ugovaretto.github.io/molekel/

Open source multi platform molecular visualization program.

Proper citation: Molekel (RRID:SCR_024122) Copy   

•   Source: SciCrunch Registry

https://www.mrtrix.org/

Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.

Proper citation: MRtrix3 (RRID:SCR_024123) Copy   

•   Source: SciCrunch Registry

https://github.com/emo-bon/MetaGOflow

Software pipeline for marine Genomic Observatories data analysis. Used to address challenges of analysis of European Marine Omics Biodiversity Observation Network data.

Proper citation: metaGOflow (RRID:SCR_023674) Copy   

•   Source: SciCrunch Registry

https://www.malvernpanalytical.com/en/support/product-support/software/microcal-peaq-itc-analysis-software-v141

Software application for isothermal titration calorimetry performed on MicroCal PEAQ instrument by Malvern.

Proper citation: Malvern Panalytical MicroCal PEAQ-ITC analysis (RRID:SCR_023795) Copy   

•   Source: SciCrunch Registry

https://pathvisio.org/

Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins.

Proper citation: PathVisio (RRID:SCR_023789) Copy   

•   Source: SciCrunch Registry

https://hints.cancer.gov/

Regularly collects nationally representative data about American public’s knowledge of, attitudes toward, and use of cancer and health related information. HINTS data are used to monitor changes in fields of health communication and health information technology and to create more effective health communication strategies across different populations. Weighted, nationally representative probability based survey of civilian, non-institutionalized adults administered by National Cancer Institute on knowledge of and attitudes toward cancer relevant information.

Proper citation: Health Information National Trends Survey (RRID:SCR_023943) 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://www.imsc.res.in/~rsidd/sigma/

Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.

Proper citation: sigma-align (RRID:SCR_024337) Copy   

•   Source: SciCrunch Registry

https://github.com/ArtRand/signalAlign

Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments,

Proper citation: signalalign (RRID:SCR_024339) 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