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BMCBI
2011

103views Artificial Intelligence» more BMCBI 2011»

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

1 years 9 days ago

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Background: Visualization of orthogonal (disjoint) or overlapping datasets is a common task in bioinformatics. Few tools exist to automate the generation of extensively-customizab...

Hanbo Chen, Paul C. Boutros

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Id	Views	Title	Status
1	103	VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R	claim
2	98	Phenotype Recognition with Combined Features and Random Subspace Classifier Ensemble	claim
3	83	SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects	claim
4	80	SNPPicker: High quality tag SNP selection across multiple populations	claim
5	72	PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment	claim
6	70	Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure	claim
7	69	Implementation of Force Distribution Analysis for Molecular Dynamics simulations	claim
8	68	Gene ontology based transfer learning for protein subcellular localization	claim
9	68	Screening synteny blocks in pairwise genome comparisons through integer programming	claim
10	66	PheMaDB: A solution for storage, retrieval, and analysis of high throughput phenotype data	claim
11	66	Predicting functionally important SNP classes based on negative selection	claim
12	65	Properties of Metabolic Graphs: Biological Organization or Representation Artifacts?	claim
13	65	pROC: an open-source package for R and S+ to analyze and compare ROC curves	claim
14	64	LabKey Server: An open source platform for scientific data integration, analysis and collaboration	claim
15	63	CNV-WebStore: Online CNV Analysis, Storage and Interpretation	claim
16	63	Identifying hypermethylated CpG islands using a quantile regression model	claim
17	61	SAQC: SNP array quality control	claim
18	61	GC/MS Based Metabolomics: Development of a Data Mining System for Metabolite Identification by using Soft Independent Modeling of Class Analogy (SIMCA)	claim
19	61	MicroSyn: A user friendly tool for detection of microsynteny in a gene family	claim
20	60	iPhy: an integrated phylogenetic workbench for supermatrix analyses	claim
21	60	RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis	claim
22	60	A quality metric for homology modeling: the H-factor	claim
23	60	Appearance frequency modulated gene set enrichment testing	claim
24	59	Using Stochastic Causal Trees to Augment Bayesian Networks for Modeling eQTL Datasets	claim
25	59	Sequential Interim Analyses of Survival Data in DNA Microarray Experiments	claim
26	59	GCOD - GeneChip Oncology Database	claim
27	59	Learning genetic epistasis using Bayesian network scoring criteria	claim
28	59	Detection of viral sequence fragments of HIV-1 subfamilies yet unknown	claim
29	58	CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis	claim
30	58	NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins	claim
31	58	Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars	claim
32	58	Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community	claim
33	58	Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform	claim
34	58	Clinical Synopsis Search in OMIM	claim
35	58	A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines	claim
36	58	Motif-guided sparse decomposition of gene expression data for regulatory module identification	claim
37	57	OrthoInspector: comprehensive orthology analysis and visual exploration	claim
38	57	Flexible taxonomic assignment of ambiguous sequencing reads	claim
39	57	PileLine: a toolbox to handle genome position information in next-generation sequencing studies	claim
40	57	Network based transcription factor analysis of regenerating axolotl limbs	claim
41	57	dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation	claim
42	56	Pathway-based analysis using reduced gene subsets in genome-wide association studies	claim
43	56	easyDAS: Automatic creation of DAS servers	claim
44	56	ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry	claim
45	56	Cell Subset Prediction for Blood Genomic Studies	claim
46	56	An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses	claim
47	56	Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms	claim
48	55	A theoretical entropy score as a single value to express inhibitor selectivity	claim
49	55	MixtureTree: a program for constructing phylogeny	claim
50	55	Shape-based peak identification for ChIP-Seq	claim
51	55	Investigating the effect of paralogs on microarray gene-set analysis	claim
52	55	Hierarchical graphs for rule-based modeling of biochemical systems	claim
53	55	A novel approach to the clustering of microarray data via nonparametric density estimation	claim
54	55	Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles	claim
55	55	AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm	claim
56	55	The dChip survival analysis module for microarray data	claim
57	55	Outer membrane proteins can be simply identified using secondary structure element alignment	claim
58	54	Estimating developmental states of tumors and normal tissues using a linear time-ordered model	claim
59	53	R2R - software to speed the depiction of aesthetic consensus RNA secondary structures	claim
60	53	PRIN, a predicted rice interactome network	claim
61	53	Genotype calling in tetraploid species from bi-allelic marker data using mixture models	claim
62	53	ChIPseqR: Analysis of ChIP-seq Experiments	claim
63	53	RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles	claim
64	53	Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies	claim
65	52	Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies	claim
66	52	CODA (CrossOver Distribution Analyzer): quantitative characterization of crossover position patterns along chromosomes	claim
67	52	Structator: fast index-based search for RNA sequence-structure patterns	claim
68	52	Multiclass classification of microarray data samples with a reduced number of genes	claim
69	52	Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and STRUCTURE	claim
70	52	Meta-analysis of gene expression microarrays with missing replicates	claim
71	51	N-gram analysis of 970 microbial organisms reveals presence of biological language models	claim
72	51	Logical Development of the Cell Ontology	claim
73	51	Context-dependent transcriptional regulations between signal transduction pathways	claim
74	51	PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination	claim
75	51	Systematic error detection in experimental high-throughput screening	claim
76	51	ASPDock: protein-protein docking algorithm using atomic solvation parameters model	claim
77	51	Tiling array data analysis: a multiscale approach using wavelets	claim
78	51	Bio: : Phylo - phyloinformatic analysis using Perl	claim
79	51	A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment	claim
80	51	Statistical learning techniques applied to epidemiology: a simulated case-control comparison study with logistic regression	claim
81	50	ENGINES: exploring single nucleotide variation in entire human genomes	claim
82	50	A Platform for Processing Expression of Short Time Series (PESTS)	claim
83	50	In-silico prediction of disorder content using hybrid sequence representation	claim
84	49	Clustering gene expression data with a penalized graph-based metric	claim
85	49	SNP-based pathway enrichment analysis for genome-wide association studies	claim
86	49	Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface	claim
87	49	nocoRNAc: Characterization of non-coding RNAs in prokaryotes	claim
88	49	Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling	claim
89	49	NeurphologyJ: an automatic neuronal morphology quantification method and its application in pharmacological discovery	claim
90	49	Empirical Bayesian models for analysing molecular serotyping microarrays	claim
91	49	Using context to improve protein domain identification	claim
92	48	Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states	claim
93	48	To aggregate or not to aggregate high-dimensional classifiers	claim
94	48	FASIMU: flexible software for flux-balance computation series in large metabolic networks	claim
95	48	Simulated evolution applied to study the genetic code optimality using a model of codon reassignments	claim
96	48	Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips	claim
97	47	The Biomedical Discourse Relation Bank	claim
98	47	Efficient alignment of pyrosequencing reads for re-sequencing applications	claim
99	47	Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions	claim
100	47	Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation	claim
101	47	A Computational Framework for Proteome-Wide Pursuit and Prediction of Metalloproteins using ICP-MS and MS/MS Data	claim
102	47	SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data	claim
103	47	MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model	claim
104	46	Revision history aware repositories of computational models of biological systems	claim
105	46	Evaluating methods for ranking differentially expressed genes applied to MicroArray Quality Control data	claim
106	46	DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI	claim
107	45	Was the Scanner Calibration Slide Used for Its Intended Purpose?	claim
108	45	Combining gene prediction methods to improve metagenomic gene annotation	claim
109	45	The PathOlogist: An Automated Tool for Pathway-Centric Analysis	claim
110	45	Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis	claim
111	45	Multivariate analysis of microarray data: differential expression and differential connection	claim
112	45	Estimation of allele frequency and association mapping using next-generation sequencing data	claim
113	45	MRCQuant- an accurate LC/MS relative isotopic quantification algorithm on TOF instruments	claim
114	45	Bioinformatics analysis of disordered proteins in prokaryotes	claim
115	45	A mutation degree model for the identification of transcriptional regulatory elements	claim
116	45	Classification of viral zoonosis through receptor pattern analysis	claim
117	44	BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs	claim
118	44	Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data	claim
119	44	Tree Pruner: An efficient tool for selecting data from a biased genetic database	claim
120	44	A Beta-Mixture Model for Dimensionality Reduction, Sample Classification and Analysis	claim
121	43	Wavelet-based identification of DNA focal genomic aberrations from single nucleotide polymorphism arrays	claim
122	43	Removing Noise From Pyrosequenced Amplicons	claim
123	43	Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays	claim
124	43	Smith-Waterman Peak Alignment for Comprehensive Two-dimensional Gas Chromatography Mass Spectrometry	claim
125	43	Computable visually observed phenotype ontological framework for plants	claim
126	43	A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models	claim
127	43	Detection of Lineage-Specific Evolutionary Changes among Primate Species	claim
128	42	Ultra-fast sequence clustering from similarity networks with SiLiX	claim
129	42	A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping	claim
130	42	Determinants of Antigenicity and Specificity in immune response for Protein Sequences	claim
131	42	compomics-utilities: an open-source Java library for computational proteomics	claim
132	41	CAPL: an efficient association software package using family and case-control data and accounting for population stratification	claim
133	41	Taxon ordering in phylogenetic trees: a workbench test	claim
134	41	FFCA: a feasibility-based method for flux coupling analysis of metabolic networks	claim
135	41	PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome	claim
136	41	AMDORAP: Non-targeted metabolic profiling based on high-resolution LC-MS	claim
137	40	A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies	claim
138	40	FIND: A new software tool and development platform for enhanced multicolor flow analysis	claim
139	40	Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure	claim
140	39	Detection of recurrent rearrangement breakpoints from copy number data	claim
141	39	Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis	claim
142	39	Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset	claim
143	39	Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library	claim
144	39	RAG: An Update to the RNA-As-Graphs Resource	claim
145	39	Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs	claim
146	39	LAVA: An Open-Source Approach To Designing LAMP (Loop-Mediated Isothermal Amplification) DNA Signatures	claim
147	38	Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing	claim
148	38	ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data	claim
149	38	A user-friendly web portal for T-Coffee on supercomputers	claim
150	38	PeakRanger: A cloud-enabled peak caller for ChIP-seq data	claim
151	38	GPCR-SSFE: A comprehensive database of G-protein-coupled receptor template predictions and homology models	claim
152	38	Conotoxin Protein Classification Using Free Scores of Words and Support Vector Machines	claim
153	38	DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning	claim
154	38	HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods	claim
155	38	PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum	claim
156	37	Robust joint analysis allowing for model uncertainty in two-stage genetic association studies	claim
157	37	Enhancements to the ADMIXTURE Algorithm for Individual Ancestry Estimation	claim
158	37	The impact of quantitative optimization of hybridization conditions on gene expression analysis	claim
159	36	A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data	claim
160	36	MINE: Module Identification in NEtworks	claim
161	35	Protein alignment algorithms with an efficient backtracking routine on multiple GPUs	claim
162	35	Binding Site Prediction for Protein-Protein Interactions and Novel Motif Discovery using Re-occurring Polypeptide Sequences	claim
163	35	Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics	claim
164	35	Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology	claim
165	34	CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation	claim
166	34	Inference of Chromosome-Specific Copy Numbers Using Population Haplotypes	claim
167	34	RegNetB: Predicting Relevant Regulator-Gene Relationships in Localized Prostate Tumor Samples	claim
168	34	Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities	claim
169	34	Gene set analysis for longitudinal gene expression data	claim
170	34	Improving pan-genome annotation using whole genome multiple alignment	claim
171	33	The Proteogenomic Mapping Tool	claim
172	33	A Simple Approach to Ranking Differentially Expressed Gene Expression Time Courses through Gaussian Process Regression	claim
173	32	Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis	claim
174	31	TreeRipper web application: towards a fully automated optical tree recognition software	claim
175	31	Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in Breast Cancer	claim
176	31	New Words in Human Mutagenesis	claim

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