Tools   Select Another Resource Report Type

http://bioinf.wehi.edu.au/affylmGUI/

R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.

Proper citation: affylmGUI (RRID:SCR_001320) Copy   

•   Source: SciCrunch Registry
  

https://www.ebi.ac.uk/jdispatcher/msa/clustalo?stype=protein

Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

Proper citation: Clustal Omega (RRID:SCR_001591) Copy   

•   Source: SciCrunch Registry
  

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

Software to detect differential expression in microarray and proteomics datasets. Its use has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

Proper citation: plgem (RRID:SCR_001355) Copy   

•   Source: SciCrunch Registry
  

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

Preprocessing and analysis software for single microarrays and microarray batches.

Proper citation: fRMA (RRID:SCR_001345) Copy   

•   Source: SciCrunch Registry
  

http://eddylab.org/software.html

Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder.

Proper citation: Eddy Lab Software (RRID:SCR_001458) Copy   

•   Source: SciCrunch Registry
  

http://tvap.genome.wustl.edu/tools/music/

A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MuSiC (RRID:SCR_008792) Copy   

•   Source: SciCrunch Registry
  

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

Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BARS (RRID:SCR_009123) 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://www.cbs.dtu.dk/services/NetOGlyc/

Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins.

Proper citation: NetOGlyc (RRID:SCR_009026) Copy   

•   Source: SciCrunch Registry
  

http://research-pub.gene.com/gmap/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.

Proper citation: GMAP (RRID:SCR_008992) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.au.tsinghua.edu.cn/software/seqsaw/

A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

Proper citation: SeqSaw (RRID:SCR_009185) Copy   

•   Source: SciCrunch Registry
  

https://github.com/SuperElastix/elastix

Software toolbox for rigid and nonrigid registration of images. Software, based on Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting.

Proper citation: elastix (RRID:SCR_009619) 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://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
  

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://mirdb.org/miRDB/

An online database for miRNA target prediction and functional annotations.

Proper citation: miRDB (RRID:SCR_010848) 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