• Nuc-ploc

  • Referenced in 14 articles [sw16471]
  • among the following nine subnuclear locations: (1) chromatin, (2) heterochromatin, (3) nuclear envelope, (4) nuclear...
  • ChromHMM

  • Referenced in 4 articles [sw29058]
  • ChromHMM: automating chromatin-state discovery and characterization. ChromHMM is software for learning and characterizing chromatin ... states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone ... models the presence or absence of each chromatin mark. The resulting model can then ... produces files with genome-wide maps of chromatin state annotations that can be directly visualized...
  • FindPeaks

  • Referenced in 7 articles [sw29575]
  • here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes...
  • F-Seq

  • Referenced in 5 articles [sw17297]
  • sites (ChIP-seq) or regions of open chromatin (DNase-seq). To intuitively summarize and display...
  • ChIPOTle

  • Referenced in 5 articles [sw20403]
  • analysis of ChIP-on-chip data. ChIPOTle (Chromatin ImmunoPrecipitation On Tiled arrays) takes advantage...
  • iNuc-STNC

  • Referenced in 5 articles [sw25364]
  • nucleosome is the fundamental unit of eukaryotic chromatin, which participates in regulating different cellular processes...
  • MDM

  • Referenced in 2 articles [sw12400]
  • MCDIST) provides functions for the analysis of chromatin interactions using MC_DIST model ... sample problem, i.e., detecting chromatin interactions from noises), Two-Step model and One-Step model ... sample problem, i.e., detecting differential chromatin interactions), based on Chromatin Interaction Analysis by Paired...
  • ChIPmix

  • Referenced in 4 articles [sw35320]
  • color ChIP–chip analysis. Motivation: Chromatin immunoprecipitation (ChIP) combined with DNA microarray is a high...
  • PeakRanger

  • Referenced in 2 articles [sw12011]
  • peak caller for ChIP-seq data. Background: Chromatin immunoprecipitation (ChIP), coupled with massively parallel short ... read sequencing (seq) is used to probe chromatin dynamics. Although there are many algorithms...
  • diffReps

  • Referenced in 2 articles [sw31661]
  • diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. ChIP ... differential sites and the other for finding chromatin modification “hotspots”. diffReps is developed in PERL...
  • csaw

  • Referenced in 3 articles [sw17944]
  • ChIP-seq data using sliding windows. Chromatin immunoprecipitation with massively parallel sequencing (ChIP...
  • PICS

  • Referenced in 3 articles [sw37329]
  • Inference for ChIP-seq. ChIP-seq combines chromatin immunoprecipitation with massively parallel short-read sequencing...
  • MrTADFinder

  • Referenced in 1 article [sw34259]
  • boundaries are marked by characteristic signatures in chromatin marks and transcription factors (TF) that ... boundary signatures change with resolution, with different chromatin features having different characteristic length scales. Furthermore ... burden is known to be coupled to chromatin structure, we examine how somatic mutations...
  • Starr

  • Referenced in 2 articles [sw20401]
  • Array Analysis of Affymetrix ChIP-chip data. Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip...
  • modENCODE

  • Referenced in 2 articles [sw22998]
  • factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing...
  • NucPosPred

  • Referenced in 2 articles [sw24770]
  • nucleosome is the basic structure of chromatin in eukaryotic cells, with essential roles...
  • HaploReg

  • Referenced in 2 articles [sw31869]
  • small indels can be visualized along with chromatin state and protein binding annotation from...
  • My5C

  • Referenced in 1 article [sw17262]
  • pools of primers to detect millions of chromatin interactions in parallel (Fig. 1). The design ... primers and the handling of large chromatin interaction maps can be daunting. To enable adoption...
  • NGS-QC

  • Referenced in 1 article [sw17301]
  • wide transcriptional activity (RNA-seq; GRO-seq), chromatin accessibility (DNase-seq, FAIRE-seq, MNase ... more recently the three-dimensional organization of chromatin (Hi-C, ChIA-PET). In systems biology...
  • iNuc-ext-PseTNC

  • Referenced in 1 article [sw27672]
  • Nucleosome is a central element of eukaryotic chromatin, which composes of histone proteins ... many eukaryotic intra-nuclear processes, for instance, chromatin structure and transcriptional regulation formation. Identification...