• csaw

  • Referenced in 3 articles [sw17944]
  • applied to both transcription factor and histone mark datasets, and, more generally, to any type...
  • Enrichr

  • Referenced in 3 articles [sw17198]
  • group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines...
  • ThIEF

  • Referenced in 1 article [sw33129]
  • ThIEF: finding genome-wide trajectories of epigenetics marks. We address the problem of comparing multiple ... maps representing nucleosome positions or specific histone marks. These maps can originate from the comparative ... genomics locations for nucleosomes or histone marks. The output is an alignment of nucleosomes/histone marks...
  • ChEA2

  • Referenced in 1 article [sw33105]
  • project for 27 different types of histone marks in 64 different human cell-lines ... mammalian transcription factor or a histone modification mark in a particular cell line, organism ... constructed regulatory networks of transcription factors and histone modifications to identify groups of regulators that...
  • DGW

  • Referenced in 1 article [sw33138]
  • shapes, thereby capturing the structure of epigenomic marks. We demonstrate the effectiveness of the approach ... start sites and splicing sites from histone marks. DGW is available as an open source...
  • WaveSeq

  • Referenced in 1 article [sw22384]
  • background noise. With the discovery of histone marks having a wide variety of enrichment patterns ... application of our algorithm to a complex histone modification data set helped make novel functional...
  • PeakRanger

  • Referenced in 2 articles [sw12011]
  • sites, or broad regions, such as histone modification marks; few can do both. Other algorithms...
  • diffReps

  • Referenced in 2 articles [sw31661]
  • used for genome-wide profiling of histone modification marks. It is of particular importance...
  • DeepChrome

  • Referenced in 1 article [sw15813]
  • novel insights about combinatorial interactions among histone modification marks, some of which have recently been...
  • ChromHMM

  • Referenced in 4 articles [sw29058]
  • such as ChIP-seq data of various histone modifications to discover de novo the major ... occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov...
  • GLPK

  • Referenced in 172 articles [sw04560]
  • The GLPK (GNU Linear Programming Kit) package is...
  • LIBSVM

  • Referenced in 1114 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • ClustalW

  • Referenced in 135 articles [sw12016]
  • CLUSTAL W: improving the sensitivity of progressive multiple...
  • CLUSTAL

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

  • Referenced in 71 articles [sw13193]
  • Muscle: multiple sequence alignment with high accuracy and...
  • Galaxy

  • Referenced in 12 articles [sw16927]
  • Galaxy: A platform for interactive large-scale genome...
  • BEDTools

  • Referenced in 12 articles [sw17302]
  • BEDTools: a flexible suite of utilities for comparing...
  • PuFFIN

  • Referenced in 2 articles [sw22390]
  • PuFFIN - a parameter-free method to build nucleosome...