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http://www.biojava.org

Project dedicated to providing Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. Sponsor: BioJava is not formally funded by any grants. Through the OBF they have received sponsorship from Sun Microsystems, Apple Computers and NESCent. The initial development of the phylogenetics module was undertaken as a Google Summer of Code 2007 project in collaboration with NESCent.

Proper citation: BioJava Project (RRID:SCR_007180) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/jist/

A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University).

Proper citation: JIST: Java Image Science Toolkit (RRID:SCR_008887) 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

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

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://github.com/TGAC/RAMPART

Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems.

Proper citation: Rampart (RRID:SCR_016742) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Rsubread.html

Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

Proper citation: Rsubread (RRID:SCR_016945) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/scran.html

Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.

Proper citation: scran (RRID:SCR_016944) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html

Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.

Proper citation: ConsensusClusterPlus (RRID:SCR_016954) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicFeatures/

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

Proper citation: GenomicFeatures (RRID:SCR_016960) Copy   

•   Source: SciCrunch Registry

https://github.com/qiicr/dcmqi

Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.

Proper citation: dcmqi (RRID:SCR_016933) Copy   

•   Source: SciCrunch Registry

https://github.com/tseemann/shovill

Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit.

Proper citation: shovill (RRID:SCR_017077) Copy   

•   Source: SciCrunch Registry

https://www.networkanalyst.ca/

Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data.

Proper citation: NetworkAnalyst (RRID:SCR_016909) Copy   

•   Source: SciCrunch Registry

http://prosightlite.northwestern.edu/

Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.

Proper citation: ProSight Lite (RRID:SCR_016908) Copy   

•   Source: SciCrunch Registry

https://github.com/PGB-LIV/VAPPER

Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections.

Proper citation: VAPPER (RRID:SCR_016993) Copy   

•   Source: SciCrunch Registry

https://github.com/CGATOxford/UMI-tools

Open source software package for handling Unique Molecular Identifiers in NGS data sets.

Proper citation: UMI-tools (RRID:SCR_017048) Copy   

•   Source: SciCrunch Registry

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

Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9.

Proper citation: rnaSPAdes (RRID:SCR_016992) Copy   

•   Source: SciCrunch Registry