Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

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Documentation for package ‘consensusSeekeR’ version 1.28.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

consensusSeekeR-package	consensusSeekeR: Detection of consensus peak regions inside a group of experiments using narrowPeak files
A549_CTCF_MYJ_NarrowPeaks_partial	Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
A549_CTCF_MYJ_Peaks_partial	Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
A549_CTCF_MYN_NarrowPeaks_partial	Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
A549_CTCF_MYN_Peaks_partial	Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
A549_FOSL2_01_NarrowPeaks_partial	Genomic regions with the greatest evidence of transcription factor binding for the FOSL2 transcription factor (for demonstration purpose)
A549_FOSL2_01_Peaks_partial	Sites with the greatest evidence of transcription factor binding for the FOSL2 transcription factor (for demonstration purpose)
A549_FOXA1_01_NarrowPeaks_partial	Genomic regions with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)
A549_FOXA1_01_Peaks_partial	Sites with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)
A549_NR3C1_CFQ_NarrowPeaks_partial	Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFQ). For demonstration purpose.
A549_NR3C1_CFQ_Peaks_partial	Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFQ). For demonstration purpose.
A549_NR3C1_CFR_NarrowPeaks_partial	Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFR). For demonstration purpose.
A549_NR3C1_CFR_Peaks_partial	Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFR). For demonstration purpose.
A549_NR3C1_CFS_NarrowPeaks_partial	Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFS). For demonstration purpose.
A549_NR3C1_CFS_Peaks_partial	Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFS). For demonstration purpose.
consensusSeekeR	consensusSeekeR: Detection of consensus peak regions inside a group of experiments using narrowPeak files
findConsensusPeakRegions	Extract regions sharing features in more than one experiment
NOrMAL_nucleosome_positions	Nucleosome positions detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.
NOrMAL_nucleosome_ranges	Ranges associated to nucleosomes detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.
NucPosSimulator_nucleosome_positions	Nucleosome positions detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.
NucPosSimulator_nucleosome_ranges	Ranges associated to nucleosomes detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.
PING_nucleosome_positions	Nucleosome positions detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.
PING_nucleosome_ranges	Ranges associated to nucleosomes detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.
readNarrowPeakFile	Extract narrow regions and peaks from a narrrowPeak file