Tools   Select Another Resource Report Type

http://apps.cytoscape.org/apps/jepetto

A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results.

Proper citation: JEPETTO (RRID:SCR_005909) Copy   

•   Source: SciCrunch Registry

https://trac.nbic.nl/passion/

A pattern growth algorithm based pileline for splice site detection in paired-end RNA-Seq data.

Proper citation: PASSion (RRID:SCR_005867) 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

https://github.com/dsturg/Spanki

A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.

Proper citation: Spanki (RRID:SCR_004469) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pasha/

A parallel short read assembler for large genomes using de Bruijn graphs.

Proper citation: PASHA (RRID:SCR_004455) Copy   

•   Source: SciCrunch Registry

http://www.leonxie.com/DeepFinder.php

Provides an comprehensive workflow of analyzing data from plant microRNA (miRNA) deep sequencing.

Proper citation: miRDeepFinder (RRID:SCR_004456) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/kdetrees/

R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

Proper citation: Kdetrees (RRID:SCR_004522) Copy   

•   Source: SciCrunch Registry

http://virome.diagcomputing.org/#view=home

A web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts. The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. The portal allows you to submit your viral metagenome to be processed through the VIROME analysis pipeline, and enable you to investigate your data via the VIROME user interface., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: VIROME (RRID:SCR_004362) Copy   

•   Source: SciCrunch Registry

http://vamps.mbl.edu/overview.php

A publicly-accessible website to measure and visualize similarities and differences between molecular profiles of complex microbial communities. The project includes visualization tools such as heat maps that simultaneously compare the taxonomic distributions of multiple datasets and 3-D charts of the frequency distributions of 16S rRNA tags. Analytical tools include Chao diversity estimates and rarefaction curves. As a service to the community, researchers have the opportunity to upload their own data to the site for private viewing with the full range of data and analysis tools. Public data can be downloaded for further analysis locally.

Proper citation: VAMPS (RRID:SCR_004483) Copy   

•   Source: SciCrunch Registry

http://snoopcgh.sourceforge.net/

A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.

Proper citation: SnoopCGH (RRID:SCR_004420) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/SCPD/

A promoter database of Saccharomyces cerevisiae. Users can explore the promoter regions of ~6000 genes and ORFs in yeast genome, annotate putative regulatory sites of all genes and ORFs, locate intergenic regions, and retrieve sequence of the promoter region. In regards to regulatory elements and transcription factors, users can provide information on transcriptionally related genes, browse matrix and consensus sequences, view the correlation between elements, observe binding affinity and expression, and look at genomewise distribution. SCPD also provides some simple but useful tools for promoter sequence analysis. Gene, consensus and matrix records may be submitted.

Proper citation: SCPD - Saccharomyces cerevisiae promoter database (RRID:SCR_004412) Copy   

•   Source: SciCrunch Registry

http://www.irisa.fr/symbiose/projects/gassst/

Software that finds global alignments of short DNA sequences against large DNA banks. It is able to perform fast gapped alignments and works well for both short and longer reads. It has been tested for reads up to 500bp.

Proper citation: GASSST (RRID:SCR_004413) Copy   

•   Source: SciCrunch Registry

http://www.trex.uqam.ca/

A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events.

Proper citation: Tree and reticulogram REConstruction (RRID:SCR_004497) Copy   

•   Source: SciCrunch Registry

http://bix.ucsd.edu/projects/singlecell/

Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria.

Proper citation: Velvet-SC (RRID:SCR_004377) Copy   

•   Source: SciCrunch Registry

http://bioinfo.unl.edu/raiphy.php

A semi-supervised metagenomic fragment classification software program that utilizes the genome signatures to characterize the DNA sequences and taxonomic classification is based on an information theoretic measure referred as Relative Abundance Index (RAI). A DNA sequence of unknown source is classified and taxonomically labeled based on the phylogenetic profiles of the previously sequenced genomes. The profiles are iteratively updated using the unknown DNA sequences and the classification results. After a few cycles, the metagenome is classified into operational taxonomic units.

Proper citation: RAIphy (RRID:SCR_004720) Copy   

•   Source: SciCrunch Registry

https://www.biodiscovery.com/products/nexus-copy-number?hsLang=en

Software package provides statistical tools. Derives copy number and BAF from variety of NGS data including WES, WGS, targeted panel, and shallow sequencing as well as Microarray data. Multifaceted desktop software for rapid discovery of genomic alterations. Accepts data from various manufacturers and technologies including Infinium GSA and CytoScan XON.

Proper citation: BioDiscovery Nexus Copy Number (RRID:SCR_004557) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/binning/ProViDE/

A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProViDE (RRID:SCR_004709) Copy   

•   Source: SciCrunch Registry

http://www.arabidopsis.org

Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.

Proper citation: TAIR (RRID:SCR_004618) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/souravc/compostbin

A DNA-composition-based binning algorithm for classifying metagenomic reads. It has the ability to accurately bin raw sequence reads without need for assembly or training. It applies principal component analysis to project the data into an informative lower-dimensional space, and then uses the normalized cut clustering algorithm on this filtered data set to classify sequences into taxon-specific bins.

Proper citation: CompostBin (RRID:SCR_004619) Copy   

•   Source: SciCrunch Registry

https://github.com/HIITMetagenomics/dsm-framework

Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples.

Proper citation: Distributed String Mining Framework (RRID:SCR_004736) Copy   

•   Source: SciCrunch Registry