• 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...

• HPeak

• Referenced in 4 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...

• 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...

• 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...

• coseg

• Referenced in 3 articles [sw19218]
• directions of changes. One example is ChIP-seq data, for which adding an up-down...

• 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...

• PePr

• Referenced in 1 article [sw34561]
• consistent or differential peaks from replicated ChIP-Seq data. Motivation: ChIP-Seq is the standard ... consistent or differential binding sites in ChIP-Seq experiments with biological replicates. PePr models read...

• 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...

• 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...