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https://bioruby.org/

Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

Proper citation: ruby-bio (RRID:SCR_024322) Copy   

•   Source: SciCrunch Registry

https://github.com/ggonnella/rgfa

Ruby library for handling GFA files.

Proper citation: rgfa (RRID:SCR_024323) Copy   

•   Source: SciCrunch Registry

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

Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures.

Proper citation: optimalcutpoints (RRID:SCR_024283) Copy   

•   Source: SciCrunch Registry

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

Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints.

Proper citation: rpact (RRID:SCR_024300) Copy   

•   Source: SciCrunch Registry

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

Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis.

Proper citation: shazam (RRID:SCR_024301) Copy   

•   Source: SciCrunch Registry

https://github.com/rrwick/Unicycler

Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline.

Proper citation: Unicycler (RRID:SCR_024380) Copy   

•   Source: SciCrunch Registry

https://github.com/dib-lab/sourmash

Software library for MinHash sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets.

Proper citation: sourmash (RRID:SCR_024347) Copy   

•   Source: SciCrunch Registry

http://tab2mage.sourceforge.net/

Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database.

Proper citation: tab2mage (RRID:SCR_024359) Copy   

•   Source: SciCrunch Registry

http://www-personal.umich.edu/~jianghui/rseq/

A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.

Proper citation: rSeq (RRID:SCR_000562) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/services/DictyOGlyc-1.1/

Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.

Proper citation: DictyOGlyc (RRID:SCR_001600) Copy   

•   Source: SciCrunch Registry

http://www.glycosciences.de/modeling/glyprot/

Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php

Proper citation: GlyProt (RRID:SCR_001560) Copy   

•   Source: SciCrunch Registry

http://phospho.elm.eu.org/

Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database.

Proper citation: Phospho.ELM (RRID:SCR_001109) Copy   

•   Source: SciCrunch Registry

http://hipipe.ncgm.sinica.edu.tw/

Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task.

Proper citation: HiPipe (RRID:SCR_001215) Copy   

•   Source: SciCrunch Registry

http://www.imagevis3d.org/

A new volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility (as shown in the images). Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation, the user can interactively explore terabyte sized data sets. Finally, the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it, such as the rendering core. This rendering core, for instance, is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with their collaborators.

Proper citation: ImageVis3D (RRID:SCR_009566) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/hclust/hclust.htm

Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HCLUST (RRID:SCR_009154) Copy   

•   Source: SciCrunch Registry

http://www.usadellab.org/cms/index.php?page=trimmomatic

Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.

Proper citation: Trimmomatic (RRID:SCR_011848) Copy   

•   Source: SciCrunch Registry

http://openbabel.org/wiki/Main_Page

Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats.

Proper citation: Open Babel (RRID:SCR_014920) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://www.gencodegenes.org

Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.

Proper citation: GENCODE (RRID:SCR_014966) Copy   

•   Source: SciCrunch Registry

https://xia2.github.io/

Data processing software that performs X-ray diffraction data processing. It handles multi-pass, multi-wavelength data sets and supports remote access to synchrotron facilities.

Proper citation: xia2 pipeline (RRID:SCR_015746) Copy   

•   Source: SciCrunch Registry

http://cab.spbu.ru/software/rnaquast/

Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.

Proper citation: rnaQUAST (RRID:SCR_016994) Copy   

•   Source: SciCrunch Registry