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https://cran.r-project.org/package=psychotree

Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models.

Proper citation: psychotree (RRID:SCR_024288) Copy   

•   Source: SciCrunch Registry

http://saint-apms.sourceforge.net/Main.html

Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: saint (RRID:SCR_024324) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/dynamicTreeCut/index.html

Software R package contains methods for detection of clusters in hierarchical clustering dendrograms.

Proper citation: dynamicTreeCut (RRID:SCR_024280) Copy   

•   Source: SciCrunch Registry

https://github.com/artic-network/readucks

Software package as Nanopore read de-multiplexer.

Proper citation: readucks (RRID:SCR_024315) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=stringi

Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing.

Proper citation: stringi (RRID:SCR_024319) Copy   

•   Source: SciCrunch Registry

http://varna.lri.fr/

Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments.

Proper citation: VARNA (RRID:SCR_024373) Copy   

•   Source: SciCrunch Registry

https://github.com/vgteam/vg#vg

Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes.

Proper citation: variation graph (RRID:SCR_024369) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/trinculo/

Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping.

Proper citation: Trinculo (RRID:SCR_024384) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=Rwave

Software R package provides environment for Time-Frequency analysis of 1-D signals.

Proper citation: rwave (RRID:SCR_024302) Copy   

•   Source: SciCrunch Registry

https://github.com/vals/umis

Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias.

Proper citation: umis (RRID:SCR_024381) Copy   

•   Source: SciCrunch Registry

https://github.com/ncbi/sra-tools/

Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces.

Proper citation: sra-toolkit (RRID:SCR_024350) Copy   

•   Source: SciCrunch Registry

http://metabarcoding.org/sumaclust

Software tool aims to cluster sequences in a way that is fast and exact at the same time.

Proper citation: sumaclust (RRID:SCR_024352) Copy   

•   Source: SciCrunch Registry

http://swissknife.sourceforge.net

Software object oriented Perl library to handle Swiss-Prot entries

Proper citation: libswiss-perl (RRID:SCR_024356) Copy   

•   Source: SciCrunch Registry

https://graphics.stanford.edu/software/volpack/

Portable software library for volume rendering.

Proper citation: VolPack (RRID:SCR_024367) Copy   

•   Source: SciCrunch Registry

http://www.homozygositymapper.org/

A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)

Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy   

•   Source: SciCrunch Registry

http://www.inmex.ca./INMEX/

A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner.

Proper citation: INMEX (RRID:SCR_004173) Copy   

•   Source: SciCrunch Registry

http://viperdb.scripps.edu/

Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: VIPERdb (RRID:SCR_002853) Copy   

•   Source: SciCrunch Registry

http://webdocs.cs.ualberta.ca/~bioinfo/PA/Sub/

Web server specialized to predict the subcellular localization of proteins using established machine learning techniques.

Proper citation: Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) Copy   

•   Source: SciCrunch Registry

http://nar.oxfordjournals.org/content/34/suppl_2/W635.long

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 9, 2016. A web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by deploying more Web wrapper agents. FASTSNP provides three options for users to submit requests. If users already have some candidate SNPs on a candidate gene, they may use Query by Candidate Gene to select the specific SNPs on the gene to perform prioritization. If users have a specified SNP or a list of SNP rsid's needs to be prioritized, they can use Query by SNP option and upload the SNP list in an Excel-format file. Finally, if users have a novel SNP sequence, FASTSNP provides Novel SNP analysis. FASTSNP will generate a SNP Function Report for each SNP. Users can export SNP data to an excel file for further genotyping processes. Other features of FASTSNP include SNP quality checking and haplotype LD information.

Proper citation: FastSNP (RRID:SCR_003140) Copy   

•   Source: SciCrunch Registry

http://www.t-profiler.org

One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool

Proper citation: T-profiler (RRID:SCR_003452) Copy   

•   Source: SciCrunch Registry