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http://www.bioconductor.org/packages/release/bioc/html/iontree.html

Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.

Proper citation: iontree (RRID:SCR_002813) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/qin/HPeak/Readme.html

A Hidden Markov Model-based algorithm for the purpose of defining genome-wide ChIP-enriched peaks in the human genome using short sequence reads.

Proper citation: HPeak (RRID:SCR_010859) Copy   

•   Source: SciCrunch Registry

http://johnsonlab.ucsf.edu/mochi.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis.

Proper citation: MochiView (RRID:SCR_000259) Copy   

•   Source: SciCrunch Registry

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

A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.

Proper citation: SOAPsplice (RRID:SCR_013253) Copy   

•   Source: SciCrunch Registry

http://www.goldenhelix.com/SNP_Variation/SNP_Analysis_Package/index.html

SNP Analysis software for basic to advanced analyses that incorporates a number of intuitive workflows to lead you beyond single marker associations. With support for case-control and quantitative traits, whole genome and candidate gene data, you can run a breadth of statistical tests under several genetic models. Advanced regression can further help elucidate even the most complex gene-gene and gene-environment interactions.

Proper citation: SNP and Variation Suite SNP Analysis (RRID:SCR_001285) Copy   

•   Source: SciCrunch Registry

https://jordan.biosci.gatech.edu/software/broadpeak/index.html

Algorithm for identifying broad peaks in diffuse ChIP-seq datasets.

Proper citation: BroadPeak (RRID:SCR_001857) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/mpg/birdsuite/birdseed.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms. This software runs a clustering algorithm and generally should be run on a sample at least 50 times. It utilizes an Expectation-Maximization (EM) algorithm to produce genotypes and confidence scores for every individual at every SNP.

Proper citation: Birdseed (RRID:SCR_001122) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/danposdoc/tutorial/dpos

Peak-calling algorithm which analyzes changes in the location, fuzziness, and occupancy at each nucleosome or protein binding position.

Proper citation: Dpos (RRID:SCR_003008) Copy   

•   Source: SciCrunch Registry

http://www.cs.ucr.edu/~yyang027/mrfseq.htm

Algorithm based on a Markov random field (MRF) model that uses additional gene coexpression data to enhance differential gene expression prediction power. It is able to call differentially expressed (DE) genes but also assign confidence scores to each inferred DE gene.

Proper citation: MRFSEQ (RRID:SCR_002972) Copy   

•   Source: SciCrunch Registry

http://dna-discovery.stanford.edu/software/rvd/

Algorithm for single nucleotide variant detection using next-generation resequencing. It estimates the error rate at each base position in the reference sequence utilizing a command-line user interface through MATLAB.

Proper citation: RVD (RRID:SCR_002635) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/SPHINX/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both "compositional" and "similarity" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPHINX (RRID:SCR_000534) Copy   

•   Source: SciCrunch Registry

http://wannovar.usc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: wANNOVAR (RRID:SCR_000565) Copy   

•   Source: SciCrunch Registry

http://www.syapse.com/

A platform and application suite for bringing together omics and clinical data.

Proper citation: Syapse (RRID:SCR_012023) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/clc-plugin/duplicate-reads-removal-plugin/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Plug-in tool to filter out duplicate reads that is specifically well-suited to handle those coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers.

Proper citation: Duplicate reads removal (RRID:SCR_000231) Copy   

•   Source: SciCrunch Registry

http://www.gogrid.com/

Commercial software company offering on-demand cloud, hybrid hosting, hosted private cloud, and dedicated infrastructure for complex needs.

Proper citation: GoGrid (RRID:SCR_013204) Copy   

•   Source: SciCrunch Registry

http://born.nii.ac.jp/

Service that retrieves disease relevant information from Twitter tweets and shows current hotspots of disease outbreaks on an interactive map. It is an ontology-driven system for detecting global health events

Proper citation: BioCaster (RRID:SCR_011869) Copy   

•   Source: SciCrunch Registry

http://www.eucalyptus.com/

Open source software for building AWS-compatible private and hybrid clouds for IT organizations in enterprises and technology businesses.

Proper citation: Eucalyptus (RRID:SCR_011872) Copy   

•   Source: SciCrunch Registry

https://www.infoquant.com/cghfusion

Software for DNA Copy Number and loss of heterozygosity (LOH) analysis designed with high-throughput diagnostic laboratories in mind.

Proper citation: CGH Fusion (RRID:SCR_000295) Copy   

•   Source: SciCrunch Registry

http://www.lab7.io/

Software to address all aspects of Next Generation Sequencing data workflow.

Proper citation: Lab7 (RRID:SCR_001210) Copy   

•   Source: SciCrunch Registry

http://www.omixon.com/hla/

An optional module in the Omixon Target application suite for HLA typing using NGS (next-generation sequencing) data that gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data.

Proper citation: Omixon Target HLA Typing (RRID:SCR_001206) Copy   

•   Source: SciCrunch Registry