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http://ngsview.sourceforge.net/

A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.

Proper citation: NGSView (RRID:SCR_005637) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/hicup/

A tool for mapping and performing quality control on Hi-C data.

Proper citation: HiCUP (RRID:SCR_005569) Copy   

•   Source: SciCrunch Registry

http://zhanglab.c2b2.columbia.edu/index.php/OLego

A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper.

Proper citation: OLego (RRID:SCR_005811) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/pepr-chip-seq/

A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions.

Proper citation: PePr (RRID:SCR_005759) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.uni-freiburg.de/Software/GraphProt/

Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.

Proper citation: GraphProt (RRID:SCR_005842) Copy   

•   Source: SciCrunch Registry

http://www-math.u-strasbg.fr/genpred/spip.php?article3

R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Cascade (RRID:SCR_005861) Copy   

•   Source: SciCrunch Registry

http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) Copy   

•   Source: SciCrunch Registry

http://mocklerlab.org/tools/1

An application for discovering potential splice junctions in high throughput sequencing (HTS) data.

Proper citation: Supersplat (RRID:SCR_009826) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/IMGT-ONTOLOGY

Ontology for immunogenetics and immunoinformatics. Provides semantic specification of terms to be used in immunogenetics and immunoinformatics and manages related knowledge, thus allowing standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. Manages the knowledge through diverse facets relying on seven axioms, IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, LOCALIZATION, ORIENTATION and OBTENTION. These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGT, the international ImMunoGeneTics information system, has been built on IMGT-ONTOLOGY. The version 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION.

Proper citation: IMGT-ONTOLOGY (RRID:SCR_010342) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPsnp (RRID:SCR_010602) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/crux/

A software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. This software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification is provided as a single executable. Crux is implemented in C and is distributed with source code freely to noncommercial users. Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification.

Proper citation: Crux tandem mass spectrometry analysis software (RRID:SCR_010648) Copy   

•   Source: SciCrunch Registry

http://snpinfo.niehs.nih.gov/

SNPinfo Web Server is a set of freely available web-based SNP selection tools where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. SNP Selection and Functional Information *Candidate Gene SNP Selection (GenePipe):SNP selection for candidate genes based on Genome Wide Association Study (GWAS) results, functional SNP prediction and Linkage Disequilibrium (LD) information. *GWAS Functional SNP Selection (GenomePipe):Functional SNP selection from SNPs that are in high LD with GWAS SNPs *GWAS SNP Selection in Linkage Loci (LinkagePipe):GWAS SNP selection in candidate genomic regions (such as linkage loci) *LD TAG SNP Selection (TagSNP):LD tag SNP selection and visualization for single or multiple populations. Finalization of SNP list from various queries. *SNP Function Prediction (FuncPred): Querying SNP function predictions and ethnic-specific allele frequencies. *SNP Information in DNA Sequence (SNPseq):Visualization of SNP related information in the context of DNA sequence. Preparing DNA Sequence for PCR Primer Design considering SNP information. Detailed information of CpG region.

Proper citation: SNPinfo Web Server (RRID:SCR_010589) Copy   

•   Source: SciCrunch Registry

http://home.gwu.edu/~wpeng/Software.htm

A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.

Proper citation: SICER (RRID:SCR_010843) Copy   

•   Source: SciCrunch Registry

http://www.netlab.uky.edu/p/bioinfo/MapSplice

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.

Proper citation: MapSplice (RRID:SCR_010844) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/mira-assembler/wiki/Home/

Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.

Proper citation: MIRA (RRID:SCR_010731) Copy   

•   Source: SciCrunch Registry

http://mocklerlab.org/tools/2

A quality-value guided de novo short read assembler.

Proper citation: QSRA (RRID:SCR_010733) Copy   

•   Source: SciCrunch Registry

http://genetics.cs.ucla.edu/harsh/

Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data.

Proper citation: HARSH (RRID:SCR_010792) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.jku.at/research/short-IBD/

Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data.

Proper citation: HapFABIA (RRID:SCR_010793) Copy   

•   Source: SciCrunch Registry

http://www.wageningenur.nl/en/show/Pedimap.htm

A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees.

Proper citation: Pedimap (RRID:SCR_010796) Copy   

•   Source: SciCrunch Registry

http://www.ngsbicocca.org/html/ceqer.html

A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads.

Proper citation: CEQer (RRID:SCR_010813) Copy   

•   Source: SciCrunch Registry