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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...
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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...
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FindPeaks
- Referenced in 7 articles
[sw29575]
- application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality...
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idr
- Referenced in 7 articles
[sw11205]
- effectiveness of our method in a ChIP-seq experiment...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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systemPipeR
- Referenced in 2 articles
[sw28861]
- sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important...
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ChromHMM
- Referenced in 3 articles
[sw29058]
- integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover...
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coseg
- Referenced in 3 articles
[sw19218]
- directions of changes. One example is ChIP-seq data, for which adding an up-down...
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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...
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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...
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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...
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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...
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Chippeakanno
- Referenced in 2 articles
[sw18996]
- Chippeakanno: a bioconductor package to annotate chip-seq and chip-chip data. The package includes...
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CSAR
- Referenced in 1 article
[sw20392]
- Statistical tools for the analysis of ChIP-seq data. Statistical tools for ChIP-seq data...