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https://rtips.cancer.gov/rtips/index.do

Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials.

Proper citation: Research-tested Intervention Programs (RTIPs) (RRID:SCR_016042) Copy   

•   Source: SciCrunch Registry

http://floresta.eead.csic.es/3dfootprint

Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.

Proper citation: 3D-footprint (RRID:SCR_015713) Copy   

•   Source: SciCrunch Registry

https://www.proteomicsdb.org/

Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository.

Proper citation: ProteomicsDB (RRID:SCR_015562) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/datasets2tools/

Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools.

Proper citation: Datasets2Tools (RRID:SCR_016174) Copy   

•   Source: SciCrunch Registry

http://www.cuilab.cn/transmir

Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data.

Proper citation: TransmiR (RRID:SCR_017499) Copy   

•   Source: SciCrunch Registry

http://bloodexposome.org

Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields.

Proper citation: Blood Exposome Database (RRID:SCR_017610) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/caf

Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site.

Proper citation: caftools (RRID:SCR_023982) Copy   

•   Source: SciCrunch Registry

http://ingenium.home.xs4all.nl/dicom.html

Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation.

Proper citation: Conquest DICOM (RRID:SCR_023993) Copy   

•   Source: SciCrunch Registry

https://github.com/pennsignals/chime

Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation.

Proper citation: CHIME (RRID:SCR_023987) Copy   

•   Source: SciCrunch Registry

https://genome.sph.umich.edu/wiki/EMMAX

Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.

Proper citation: EMMAX (RRID:SCR_024012) Copy   

•   Source: SciCrunch Registry

http://www.dicompyler.com/

Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer.

Proper citation: dicompyler (RRID:SCR_024006) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/foreign/index.html

Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.

Proper citation: foreign (RRID:SCR_024025) Copy   

•   Source: SciCrunch Registry

https://github.com/rrwick/Deepbinner

Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads.

Proper citation: Deepbinner (RRID:SCR_024001) Copy   

•   Source: SciCrunch Registry

http://amide.sourceforge.net/index.html

Software tool for viewing, analyzing, and registering volumetric medical imaging data sets. It has been written on top of GTK+ and runs on any system that supports this toolkit (Linux, Windows, Mac OS X, etc.). The program incorporates automatic non-orthogonal data reslicing, allowing multiple data set to be fused without imposed constraints on the dimensions, anisotrophy, or voxel sizes of the data. Additional features include 3D ROI (ellipses, cylinders, boxes, and isocontours), multi-slice viewing, volume rendering, and data importing through the (X)MedCon library.

Proper citation: amide (RRID:SCR_005940) Copy   

•   Source: SciCrunch Registry

http://www.seqexpress.com/

A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options.

Proper citation: SeqExpress (RRID:SCR_007075) Copy   

•   Source: SciCrunch Registry

https://database.riken.jp/sw/en/The_RIKEN_integrated_database_of_mammals/ria254i/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019.
A database that integrates not only RIKEN''''s original large-scale mammalian databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists'''' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.

Proper citation: RIKEN integrated database of mammals (RRID:SCR_006890) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/epigenomix.html

Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.

Proper citation: epigenomix (RRID:SCR_006407) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapaligner.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPaligner/soap2 (RRID:SCR_005503) Copy   

•   Source: SciCrunch Registry

http://www.pedigree-draw.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software)

Proper citation: Pedigree-Draw (RRID:SCR_008302) Copy   

•   Source: SciCrunch Registry

http://www.ch.embnet.org/software/COILS_form.html

COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.

Proper citation: COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) Copy   

•   Source: SciCrunch Registry