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http://acgt.cs.tau.ac.il/modent/
A computational tool that reconstructs gene regulatory networks from high throughput experimental data.
Proper citation: MODENT - A Tool For Reconstructing Gene Regulatory Networks (RRID:SCR_000220) Copy
http://www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures.
Proper citation: GOLD (RRID:SCR_000188) Copy
https://omictools.com/context-likelihood-of-relatedness-tool
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software that infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles.
Proper citation: Context Likelihood of Relatedness (RRID:SCR_000216) Copy
https://github.com/vahuynh/dynGENIE3
An algorithm for the inference of gene regulatory networks from expression data.
Proper citation: GENIE3 (RRID:SCR_000217) Copy
http://bonneaulab.bio.nyu.edu/networks.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for learning parsimonious regulatory networks from systems biology data sets de novo. Software that utilizes inference algorithm to model genetic regulatory networks.Inferelator 2.0 is scalable framework for reconstruction of dynamic regulatory network models., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Inferelator (RRID:SCR_000218) Copy
http://cran.r-project.org/web/packages/c3net/index.html
Software package that allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET.
Proper citation: c3net (RRID:SCR_000212) Copy
http://www.uniklinikum-saarland.de/einrichtungen/fachrichtungen/humangenetik/software/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites.
Proper citation: GraBCas (RRID:SCR_000205) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software package for the prediction of calpain cleavage sites.
Proper citation: GPS-Calpain Cleavage Detector (RRID:SCR_000202) Copy
http://ribopicker.sourceforge.net/
Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.
Proper citation: riboPicker (RRID:SCR_000360) Copy
A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.
Proper citation: ARACHNE (RRID:SCR_000351) Copy
http://parsecnv.sourceforge.net/
Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.
Proper citation: ParseCNV (RRID:SCR_000355) Copy
http://sourceforge.net/projects/kinannote/
Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.
Proper citation: Kinannote (RRID:SCR_000352) Copy
http://sourceforge.net/projects/jnomics/
A collection of cloud-scale DNA sequence analysis tools.
Proper citation: Jnomics (RRID:SCR_000348) Copy
A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks.
Proper citation: ABrowse (RRID:SCR_000345) Copy
http://icbi.at/software/gpviz/gpviz.shtml
A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants.
Proper citation: GPViz (RRID:SCR_000346) Copy
http://www.bioconductor.org/packages/release/bioc/html/iASeq.html
Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.
Proper citation: iASeq (RRID:SCR_000420) Copy
http://cran.r-project.org/web/packages/PSCBS/
Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Proper citation: PSCBS (RRID:SCR_000417) Copy
http://www.bioconductor.org/packages/release/bioc/html/rTANDEM.html
An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.
Proper citation: rTANDEM (RRID:SCR_000409) Copy
https://sites.google.com/site/beckerjeremie/home/nucleofinder
A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.
Proper citation: NucleoFinder (RRID:SCR_000368) Copy
https://github.com/yongchao/flowPeaks
Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Proper citation: flowPeaks (RRID:SCR_000407) Copy
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