• Bioconductor

  • Referenced in 305 articles [sw04205]
  • analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language...
  • PMA

  • Referenced in 113 articles [sw19126]
  • canonical correlation analysis, with applications to genomic data. Statistical Applications in Genetics and Molecular Biology...
  • ArrayExpress

  • Referenced in 40 articles [sw29723]
  • ArrayExpress - functional genomics data. ArrayExpress Archive of Functional Genomics Data stores data from high-throughput ... functional genomics experiments, and provides these data for reuse to the research community...
  • clustervalidation

  • Referenced in 31 articles [sw34195]
  • Computational cluster validation in post-genomic data analysis. Results: This review paper aims to familiarize ... focus on their application to post-genomic data analysis. Synthetic and real biological datasets...
  • PatternHunter

  • Referenced in 36 articles [sw20963]
  • which are then extended. The exploding genomic data growth presents a dilemma for DNA homology...
  • iRSpot-TNCPseAAC

  • Referenced in 31 articles [sw22412]
  • With the ever-increasing amount of genome sequence data in the postgenomic era, computational methods ... meiotic recombination and the process of genome evolution as well. To meet the need...
  • SMART

  • Referenced in 16 articles [sw17187]
  • SMART 4.0: towards genomic data integration. SMART (Simple Modular Architecture Research Tool ... centred on the integration of data from completed metazoan genomes. SMART now uses predicted proteins...
  • GEOquery

  • Referenced in 9 articles [sw17285]
  • become a standard molecular biology tool. Experimental data have been generated on a huge number ... analysis and comprehension of genomic data. The tools contained in the BioConductor project represent many ... analysis of microarray and genomics data. We have developed a software tool that allows access ... conclusions can be drawn from published genomic data. Availability: GEOquery is available as part...
  • edgeR

  • Referenced in 48 articles [sw06936]
  • differential expression analysis of digital gene expression data. t is expected that emerging digital gene ... future for many functional genomics applications. One of the fundamental data analysis tasks, especially...
  • GenMAPP

  • Referenced in 8 articles [sw12317]
  • visualize gene expression and other genomic data on maps representing biological pathways and groupings ... global analysis of gene expression or genomic data in the context of hundreds of pathway ... export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP ... MAPP files based on user-imported genomic data. Query data against MAPPs and the GeneOntology...
  • GATK

  • Referenced in 15 articles [sw12019]
  • sequencing data. Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project ... However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly ... manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK ... provides a small but rich set of data access patterns that encompass the majority...
  • BioHMM

  • Referenced in 13 articles [sw10920]
  • method (BioHMM) for segmenting array comparative genomic hybridization data into states with the same underlying...
  • RSEM

  • Referenced in 11 articles [sw17160]
  • quantification from RNA-Seq data with or without a reference genome. Background ... data. In contrast to other existing tools, the software does not require a reference genome ... species without sequenced genomes. On simulated and real data sets, RSEM has superior or comparable ... data. As it does not rely on the existence of a reference genome...
  • JIVE

  • Referenced in 12 articles [sw09511]
  • objects. In particular, The Cancer Genome Atlas (TCGA) includes data from several diverse genomic technologies ... variation for the integrated analysis of such data sets. The decomposition consists of three terms...
  • SPAdes

  • Referenced in 12 articles [sw17004]
  • complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single ... multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that...
  • BioProspector

  • Referenced in 29 articles [sw09375]
  • throughput genome sequencing and gene expression techniques gives rise to the demand for data-mining ... sequences or pre-computed from the whole genome sequences. A new motif scoring function ... find s54 motif from M. xanthus genome, many B. subtilis motifs from DBTBS collection ... promoters, and motifs from yeast expression data...
  • CVTree3

  • Referenced in 7 articles [sw22015]
  • each other and ultimately follow the genome data. With the number of sequenced genomes reaching...
  • ranger

  • Referenced in 29 articles [sw14498]
  • random forests to analyze data on the scale of a genome-wide association study...
  • PennCNV

  • Referenced in 16 articles [sw19390]
  • number variation detection in whole-genome SNP genotyping data. Comprehensive identification and cataloging of copy ... where available. We applied PennCNV to genotyping data generated for 112 HapMap individuals; on average ... results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density...
  • marrayClasses

  • Referenced in 7 articles [sw08346]
  • microarray-specific R objects for storing these data. Functions for diagnostic plots of microarray spot ... computing framework for the analysis of genomic data...