• BayesPeak

  • Referenced in 7 articles [sw18843]
  • BayesPeak - an R package for analysing chip-seq data. Motivation: Identification of genomic regions ... interest in ChIP-seq data, commonly referred to as peak-calling, aims to find...
  • FindPeaks

  • Referenced in 7 articles [sw29575]
  • application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality...
  • idr

  • Referenced in 7 articles [sw11205]
  • effectiveness of our method in a ChIP-seq experiment...
  • DREME

  • Referenced in 3 articles [sw17299]
  • DREME: motif discovery in transcription factor ChIP-seq data. Motivation: Transcription factor (TF) ChIP ... seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery. Most ... optimized to analyze very large ChIP-seq datasets in minutes. Using DREME, we discover ... mouse erythrocyte and human cell line ChIP-seq datasets. For example, in mESC ChIP...
  • HPeak

  • Referenced in 3 articles [sw29576]
  • defining read-enriched regions in ChIP-Seq data. Results: Here we introduce HPeak ... based Peak-finding algorithm for analyzing ChIP-Seq data to identify protein-interacting genomic regions ... contrast to the majority of available ChIP-Seq analysis software packages, HPeak is a model ... available ChIP-Seq analysis approaches. Additionally, in comparison to the ChIP-chip assay, ChIP...
  • ChIPDiff

  • Referenced in 4 articles [sw31704]
  • Histone Modification Sites Identified by ChIP-seq. ChIPDiff provides a solution for the identification ... Modification Sites (DHMSs) by comparing two ChIP-seq libraries...
  • F-Seq

  • Referenced in 5 articles [sw17297]
  • Seq: a feature density estimator for high-throughput sequence tags. Summary: Tag sequencing using high ... such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase...
  • csaw

  • Referenced in 3 articles [sw17944]
  • package for differential binding analysis of ChIP-seq data using sliding windows. Chromatin immunoprecipitation with ... massively parallel sequencing (ChIP-seq) is widely used to identify binding sites for a target...
  • diffReps

  • Referenced in 2 articles [sw31661]
  • detecting differential chromatin modification sites from ChIP-seq data with biological replicates. ChIP ... particular importance to compare ChIP-seq data of two different conditions, such as disease ... detect those differential sites from ChIP-seq data, with or without biological replicates. In addition ... have developed two useful tools for ChIP-seq analysis in the diffReps package...
  • DIME

  • Referenced in 2 articles [sw18855]
  • DIME: R-package for identifying differential chip-seq based on an ensemble of mixture models ... binding sites between two conditions using ChIP-seq data. It considers a collection of finite ... statistical approach. In addition to ChIP-seq, DIME is also applicable to data from other...
  • PeakRanger

  • Referenced in 2 articles [sw12011]
  • cloud-enabled 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 ... many algorithms to call peaks from ChIP-seq datasets, most are tuned either to handle...
  • systemPipeR

  • Referenced in 2 articles [sw28861]
  • sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important...
  • ChromHMM

  • Referenced in 3 articles [sw29058]
  • integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover...
  • ChIP-PaM

  • Referenced in 1 article [sw22385]
  • identify protein-DNA interaction using ChIP-Seq data. BACKGROUND: ChIP-Seq is a powerful tool ... transcription factor binding sites identified from ChIP-Seq data significantly limit its application. RESULTS: Here ... identifying transcription factor target regions in ChIP-Seq datasets. This algorithm makes full ... binding on the basis of ChIP-Seq data only. An analysis of real genomic data...
  • Nebula

  • Referenced in 1 article [sw16944]
  • Nebula — a web-server for advanced ChIP-seq data analysis. Motivation: ChIP-seq consists ... perform a complete bioinformatics analysis of ChIP-seq data. Results: Nebula was designed for both ... service that provides an advanced ChIP-seq analysis pipeline providing ready-to-publish results...
  • ChEA2

  • Referenced in 1 article [sw33105]
  • Experiments to Decode the Transcription Regulome. ChIP-seq experiments provide a plethora of data regarding ... transcription regulation in mammalian cells. Integrating ChIP-seq studies into a computable resource is potentially ... database where we convert results from ChIP-seq experiments into gene-set libraries. The manual...
  • coseg

  • Referenced in 2 articles [sw19218]
  • directions of changes. One example is ChIP-seq data, for which adding an up-down...
  • Chippeakanno

  • Referenced in 2 articles [sw18996]
  • Chippeakanno: a bioconductor package to annotate chip-seq and chip-chip data. The package includes...
  • CSAR

  • Referenced in 1 article [sw20392]
  • Statistical tools for the analysis of ChIP-seq data. Statistical tools for ChIP-seq data...
  • MMDiff

  • Referenced in 1 article [sw20380]
  • Bioconductor package MMDiff: Statistical Testing for ChIP-Seq data sets. This package detects statistically significant ... between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences...