TSS_galonska
(Package: DChIPRep) :
TSS around called peak regions from Galonska et. al.
This data contains mouse mm9 TSS close to called peak regions for H3Kme3 from Galonksa et al. The original peak lists are from are from GEO (GSE56312) and have been merged into a common peaklist and then annotated to the closest mm9 TSS using annotatePeakInBatch.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: TSS_galonska
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chip_galonska
(Package: DChIPRep) :
Another example ChIP data set that can be used
The containes the H3Kme3 data in the serum and 24h_2i conditions from Galonska et. al., 2015 as well as the whole cell extract data, which is treated as input for all four samples. The data were downloaded from the SRA at the european nucleotide archive (ENA, accession PRJNA242892). The reads were aligned ot the mm9 reference genome using bowtie2 (Langmead and Salzberg, 2012) with default options. Then, filtering of unmapped, low mapping quality (< 10), duplicated and multi-mapping reads was performed with Picard tools. The fragment length was inferred using cross correlation plots from SPP (Kharchenko, et. al., 2008).
● Data Source:
BioConductor
● Keywords: datasets
● Alias: chip_galonska
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An example ChIP data set that can be used with importDataFromMatrices. Its associated sample table can be accessed via data(data(exampleSampleTable).
● Data Source:
BioConductor
● Keywords: datasets
● Alias: exampleChipData
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An example input data set that can be used with importDataFromMatrices. Its associated sample table can be accessed via data(data(exampleSampleTable).
● Data Source:
BioConductor
● Keywords: datasets
● Alias: exampleInputData
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An example sample table
● Data Source:
BioConductor
● Keywords: datasets
● Alias: exampleSampleTable
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input_galonska
(Package: DChIPRep) :
Another example Input data set that can be used
The matrix containes the whole cell extract (WCE) data for H3Kme3 from the paper in each of the four columns, since this is the only inpu data provided for all 4 samples. For additional information see the documentation of chip_galonska.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: input_galonska
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sample_table_galonska
(Package: DChIPRep) :
Another example sample table based on data from rom Galonska et. al., 2015.
This table contains the sample annotation for the H3Kme3 data from Galonska et. al., 2015. For additional information see the documentation of chip_galonska.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: sample_table_galonska
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testData
(Package: DChIPRep) :
A test DESeqDataSet
test data to check the functions
● Data Source:
BioConductor
● Keywords: datasets
● Alias: testData
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