Tools
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Revision as of 21:28, 31 March 2014
Below we highlight some of our tools and data sets. For an overview of tool-centric lab publications see our tools papers page. The source code of many of our tools in available on our lab Github page.
Contents |
Tools portals
MolMovDB
Tool Name Description
MolMovDBThis describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis.
Pseudogene.org
Tool Name Description
Pseudogene.org]Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.
Networks
Tool Name Description
NetworksThe Gerstein lab has been a pioneer in applying network analysis to generate knowledge form large-scale experiments.To this end, we have developed a portal for our network research.
Structural Variants (SV)
Tool Name Description
Structural VariantsStructural Variations (SVs) and Copy Number Variations (CNVs) are a major source of genetic variation. our analysis tools are available in this portal.
Genome Technology Tools
Structural Variation
Tool Name Release Date Description CNVnator 2013 An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. AGE 2013 AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
Functional Annotation
Tool Name Release Date Description FunSeq 2013 This site can be used to automatically score and annotate disease-causing potential of SNVs, particularly the non-coding ones. It can be used on cancer and personal genomes. It also contains a downloadable tool. VAT
Github repo2012 A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.
RNA-seq
Tool Name Release Date Description FusionSeq
Github repo2011 FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data. ACT 2011 The aggregation and correlation toolbox (ACT) is an aggregation and correlation toolbox for analyses of genome tracks. IQseq 2010 A tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene. RSEQtools 2010 A suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF was developed to address privacy concerns associated with the potential for mRNA sequence reads to identify and genetically characterise specific individuals; it is a compact data summary format that enables anonymization of confidential sequence information, while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.
ChIP
Tool Name Release Date Description BoCaTFBS 2006 A boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. This tool is based on a data mining approach combining noisy data from ChIP-chip experiments with known binding site patterns. BoCaTFBS uses boosted cascades of classifiers for optimum efficiency, in which components are alternating decision trees; it exploits interpositional correlations; and it explicitly integrates massive negative information from ChIP-chip experiments. PeakSeq 2009 A tool for calling peaks corresponding to transcription factor binding sites from ChIP-Seq data scored against a matched control such as Input DNA. PeakSeq employs a two-pass strategy in which putative binding sites are first identified in order to compensate for genomic variation in the 'mappability' of sequences, before a second pass filters out sites not significantly enriched compared to the normalized control, computing precise enrichments and significances. Our scoring procedure enables us to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information.
Allele-specific effects
Tool Name Release Date Description AlleleSeq 2011 The AlleleSeq is a computational pipeline that is used to study allele-specific expression (ASE) and allele specific binding (ASB). The pipeline first constructs a diploid personal genome sequence, then map RNA-seq and ChIP-seq functional genomic data onto this personal genome. Consequently, locations where there are differences in number of mapped reads between maternally- and paternally-derived sequences can be identified and these provide evidence for allele-specific events.
Microarrays & Proteomics
Tool Name Release Date Description motips 2003 MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains. ExpressYourself 2003 An interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data. PARE 2007 (Protein Abundance and mRNA Expression). A tool for comparing protein abundance and mRNA expression data. In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which are potentially worth further examination. 3vee 1998 3vee is collection of program for the assessment of volumes in protein files.
geometry 1999 calculation of geometrical quantities associated with macromolecular structures and their motions
Clustering
Tool Name Release Date Description Local Clustering 2001 A new algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data is available as C source code.
Network Tools
Tool Name Release Date Description TopNet 2004 An automated web tool designed to calculate topological parameters and compare different sub-networks for any given network. tYNA 2006 (TopNet-like Yale Network Analyzer). A Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks etc.
Evolution Tools
Tool Name Release Date Description Coevolution analysis of protein residues 2008 An integrated online system that enables comparative analyses of residue coevolution with a comprehensive set of commonly used scoring functions, including Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation (ELSC), mutual information and correlation-based methods.
Structural Biology Tools
Tool Name Release Date Description SPINE 2001 A laboratory-information management system (LIMS) for the NorthEast Structural Genomics Consortium. The online version is restricted to consortium users, but most of the code is freely available for download. Macromolecular Packing Tools 1994-2009 A number of programs for calculating properties of protein and nucleic acid structures have been collected into a single distribution. Included are a library of utility functions for dealing with structures, and a convenient interactive command-line interpreter. HIT 2006 (Helix Interaction Tool). A web-based comprehensive package of tools for analyzing helix-helix interactions in proteins.
Data sets
Tool Name Release Date Description BreakDB 2008 This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.
Other
Tool Name Release Date Description PubNet 2005 A web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis.