Tools   Select Another Resource Report Type

http://www.thegpm.org/tandem/

Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences.

Proper citation: X!Tandem (RRID:SCR_015645) Copy   

•   Source: SciCrunch Registry

https://jasp-stats.org/

Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests.

Proper citation: JASP (RRID:SCR_015823) Copy   

•   Source: SciCrunch Registry

http://apps.cytoscape.org/apps/mcode

Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks.

Proper citation: MCODE (RRID:SCR_015828) Copy   

•   Source: SciCrunch Registry

https://www.github.com/arq5x/poretools

Software toolkit for analyzing nanopore sequence data.

Proper citation: Poretools (RRID:SCR_015879) Copy   

•   Source: SciCrunch Registry

http://snf-515788.vm.okeanos.grnet.gr/

Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DIANA-mirPath (RRID:SCR_017354) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/epik

Software program for pKa prediction and protonation state generation for drug like molecules.

Proper citation: Epik (RRID:SCR_016745) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/ligprep

Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures.

Proper citation: Ligprep (RRID:SCR_016746) Copy   

•   Source: SciCrunch Registry

https://networkx.github.io/

Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Proper citation: NetworkX (RRID:SCR_016864) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/BRASS

Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements.

Proper citation: BRASS (RRID:SCR_017091) Copy   

•   Source: SciCrunch Registry

https://www.google.com/

American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook.

Proper citation: Google (RRID:SCR_017097) Copy   

•   Source: SciCrunch Registry

https://github.com/aldenleung/OMTools

Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles.

Proper citation: OMTools (RRID:SCR_017143) Copy   

•   Source: SciCrunch Registry

http://mummer.sourceforge.net/

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

Proper citation: MUMmer (RRID:SCR_018171) Copy   

•   Source: SciCrunch Registry

https://www.mrc-bsu.cam.ac.uk/software/bugs/the-bugs-project-winbugs/

Software package for Bayesian analysis of complex statistical models using Markov chain Monte Carlo methods.

Proper citation: WinBUGS (RRID:SCR_018516) Copy   

•   Source: SciCrunch Registry

http://autodock.scripps.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock.

Proper citation: Autogrid (RRID:SCR_015982) Copy   

•   Source: SciCrunch Registry

http://www.scandb.org/newinterface/about.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SCAN (RRID:SCR_005185) Copy   

•   Source: SciCrunch Registry

http://www-stat.stanford.edu/~tibs/SAM/

Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments.

Proper citation: SAM (RRID:SCR_010951) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.vub.ac.be/databases/databases.html

Downloadable data set designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use. Currently, the database contains 2 sets, each consisting of a number of subsets with related sequences. It''s main features are: * Covers the entire known fold space (SCOP classification), with subsets provided by the ASTRAL compendium * All structures have high quality, with 100% resolved residues * Structure alignments have been derived carefully, using both SOFI and CE, and Relaxed Transitive Alignment * At most 25 sequences in each subset to avoid overrepresentation of large folds* Automated running, archiving and scoring of programs through a few Perl scripts The Twilight Zone set is divided into sequence groups that each represent a SCOP fold. All sequences within a group share a pairwise Blast e-value of at least 1, for a theoretical database size of 100 million residues. Sequence similarity is thus very low, between 0-25% identity, and a (traceable) common evolutionary origin cannot be established between most pairs even though their structures are (distantly) similar. This set therefore represents the worst case scenario for sequence alignment, which unfortunately is also the most frequent one, as most related sequences share less than 25% identity. The Superfamilies set consists of groups that each represent a SCOP superfamily, and therefore contain sequences with a (putative) common evolutionary origin. However, they share at most 50% identity, which is still challenging for any sequence alignment algorithm. Frequently, alignments are performed to establish whether or not sequences are related. To benchmark this, a second version of both the Twilight Zone and the Superfamilies set is provided, in which to each alignment problem a number of false positives, i.e. sequences not related to the original set, are added. Database specifications: * Current version: 1.65 (concurrent with PDB, SCOP and ASTRAL) * Twilight Zone set (with false positives): 209 groups, 1740 (3280) sequences, 10667 (44056) related pairs * Superfamilies set (with false positives): 425 groups, 3280 (6526) sequences, 19092 (79095) related pairs

Proper citation: SABmark (RRID:SCR_011817) Copy   

•   Source: SciCrunch Registry

http://www.biogazelle.com/qbaseplus

Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology.

Proper citation: qBasePLUS (RRID:SCR_003370) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://broadinstitute.github.io/picard/

Java toolset for working with next generation sequencing data in the BAM format.

Proper citation: Picard (RRID:SCR_006525) Copy   

•   Source: SciCrunch Registry

https://www.statease.com/software/design-expert/

Statistical software package from Stat-Ease Inc. to perform design of experiments. Offers comparative tests, screening, characterization, optimization, robust parameter design, mixture designs and combined designs.

Proper citation: Design-Expert (RRID:SCR_022671) Copy   

•   Source: SciCrunch Registry