normR: Regime enrichment calling for ChIP-seq data
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Summary
The statistical framework “normR” achieves a sensitive normalization by accounting for the effect of putative protein-bound regions on the overall read statistics by demonstrating normR’s suitability in three studies.
- Type
- preprint
- Published
- 2016-10-25
- Cited by
- 11
- References
- 90
- Access
- Open access
- OpenAlex
- https://openalex.org/W2538741894
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:64377573
Keywords
H3K4me3, Normalization (sociology), Bioconductor, Chip, Computer science
References
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- ChromHMM: automating chromatin state discovery and characterization
- Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments
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- An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data
- Hyperconserved CpG domains underlie Polycomb-binding sites
- DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
- Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data
- A promoter-level mammalian expression atlas
- Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling
- A comparison of control samples for ChIP-seq of histone modifications
- Strategies for immortalization of primary hepatocytes
- E2F-4 and E2F-5, two members of the E2F family, are expressed in the early phases of the cell cycle.
- The N-terminus of histone H3 is required for de novo DNA methylation in chromatin
- Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing
- Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
- Integrative Genomics Viewer
- Origins and functional impact of copy number variation in the human genome
- Transcriptome and genome sequencing uncovers functional variation in humans
- Histone modification
Cited by
- Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin
- Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
- Solving the transcription start site identification problem with ADAPT-CAGE: a Machine Learning algorithm for the analysis of CAGE data
- Spatial rearrangement of the Streptomyces venezuelae linear chromosome during sporogenic development
- Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection
- Chromatin in 3D distinguishes dMes-4/NSD and Hypb/dSet2 in protecting genes from H3K27me3 silencing
- Reversible repression of inducible genes by Polycomb Repressive Complex 2 and H3K27me3 in Drosophila melanogaster
- Regional Conservation and Transcriptional Regulation of Tumor-Associated Genes by macroH2A1 Deposition in Mammalian Cells
- SMC modulates ParB engagement in segregation complexes in streptomyces
- Strawberry Notch 1 Acts as a Transcriptional Regulator Driving Oncogenic Programs in Liver Carcinogenesis
- SMC modulates ParB engagement in segregation complexes in Streptomyces
- Two Contrasting Classes of Nucleolus-Associated Domains in Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin [preprint] Mouse Fibroblast Heterochromatin [preprint]
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