• iNuc-PseKNC

  • Referenced in 31 articles [sw16607]
  • PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple ... nucleotide composition. Motivation: Nucleosome positioning participates in many cellular activities and plays significant roles ... automated methods for rapidly and effectively identifying nucleosome positioning. Although some computational methods were proposed ... might play important roles in determining the nucleosome positioning on a DNA sequence. Results: Here...
  • iNuc-PhysChem

  • Referenced in 24 articles [sw22453]
  • PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties. Nucleosome positioning has important ... made in this area, the rules defining nucleosome positioning is still elusive and debated ... twelve DNA physicochemical features between the nucleosomal and linker sequences in the Saccharomyces cerevisiae genome ... found that nucleosomal sequences have some position-specific physicochemical features, which can be used...
  • iNuc-STNC

  • Referenced in 5 articles [sw25364]
  • sequence-based predictor for identification of nucleosome positioning in genomes by extending the concept ... SAAC and Chou’s PseAAC. The nucleosome is the fundamental unit of eukaryotic chromatin, which ... order to identify accurately and reliably nucleosome positioning in genomes. In this proposed model...
  • BayesPeak

  • Referenced in 8 articles [sw18843]
  • transcription factor binding sites, modified histones or nucleosomes. The BayesPeak algorithm was developed to model...
  • PuFFIN

  • Referenced in 2 articles [sw22390]
  • PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads. BACKGROUND ... short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes ... their data (e.g., the maximum allowed nucleosome overlap or legal ranges for the fragment sizes ... genome-wide set of non-overlapping nucleosomes without any user-defined parameter. This feature makes...
  • NucPosPred

  • Referenced in 2 articles [sw24770]
  • NucPosPred: predicting species-specific genomic nucleosome positioning via four different modes of general PseKNC ... nucleosome is the basic structure of chromatin in eukaryotic cells, with essential roles ... splicing. Because of the importance of nucleosomes, the factors that determine their positioning within genomes ... should be investigated. High-resolution nucleosome-positioning maps are now available for organisms including...
  • ThIEF

  • Referenced in 1 article [sw33129]
  • comparing multiple genome-wide maps representing nucleosome positions or specific histone marks. These maps ... list of genomics locations for nucleosomes or histone marks. The output is an alignment ... applications on the analysis of temporal nucleosome maps for the human malaria parasite ... accurately predict the position of stable nucleosomes (i.e., nucleosomes present in all time points...
  • iNuc-ext-PseTNC

  • Referenced in 1 article [sw27672]
  • efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou ... PseAAC to pseudo-tri-nucleotide composition. Nucleosome is a central element of eukaryotic chromatin, which ... structure and transcriptional regulation formation. Identification of nucleosome positioning via wet lab is difficult ... PseTNC” is developed to identify the nucleosome positioning in genomes accurately. In this predictor...
  • nucleR

  • Referenced in 1 article [sw22389]
  • package nucleR: Nucleosome positioning package for R. Nucleosome positioning for Tiling Arrays and NGS experiments...
  • nucleoSim

  • Referenced in 1 article [sw22391]
  • package nucleoSim: Generate synthetic nucleosome maps. This package can generate a synthetic map with reads ... covering the nucleosome regions as well as a synthetic map with forward and reverse reads...
  • plot2DO

  • Referenced in 1 article [sw37588]
  • most used method to investigate nucleosome organization on a genome-wide scale. We present plot2DO ... data, and for visualizing the distribution of nucleosomes near the functional regions of the genome...
  • VplotR

  • Referenced in 1 article [sw37587]
  • fragment density plots to accurately map nucleosome occupancy along the genome. VplotR...
  • PING

  • Referenced in 0 articles [sw32043]
  • PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data. MNase ... identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible ... open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase ... uses a model-based approach, which enables nucleosome predictions even in the presence...
  • R

  • Referenced in 9810 articles [sw00771]
  • R is a language and environment for statistical...
  • GLPK

  • Referenced in 181 articles [sw04560]
  • The GLPK (GNU Linear Programming Kit) package is...
  • LIBSVM

  • Referenced in 1184 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • Stata

  • Referenced in 837 articles [sw06029]
  • Stata is a complete, integrated statistical package that...
  • BioProspector

  • Referenced in 29 articles [sw09375]
  • BioProspector: discovering conserved DNA motifs in upstream regulatory...
  • ClustalW

  • Referenced in 138 articles [sw12016]
  • CLUSTAL W: improving the sensitivity of progressive multiple...
  • CLUSTAL

  • Referenced in 18 articles [sw12750]
  • CLUSTAL: a package for performing multiple sequence alignment...