deepTools2: a next generation web server for deep-sequencing data analysis
Citations
7,892 citations
Cites methods from "deepTools2: a next generation web s..."
...We created normalized read coverage tracks (bigwig format) for each BAM file using the program bamCoverage in the deepTools package [Ramı́rez et al., 2016] with the binSize parameter set to 1 and using the reads per kilobase per million mapped reads (RPKM) normalization option....
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...1.2 Ramı́rez et al., 2016 https://github.com/deeptools/deepTools GOstats v2....
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...We created normalized read coverage tracks (bigwig format) for each BAM file using the program bamCoverage in the deepTools package [Ramı́rez et al., 2016] with the binSize parameter set to 1 and using the reads per kilobase per million mapped reads (RPKM) normalization option. e10 Cell 177,…...
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4,409 citations
2,601 citations
2,037 citations
Cites methods from "deepTools2: a next generation web s..."
...We created normalized read coverage tracks (bigwig format) for each BAM file using the program bamCoverage in the deepTools package [Ramı́rez et al., 2016] with the binSize parameter set to 1 and using the reads per kilobase per million mapped reads (RPKM) normalization option....
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846 citations
References
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Additional excerpts
...The rapidly increasing diversity of experimental assays using high-throughput sequencing has led to a concomitant increase in the number of analysis packages that allow for insightful visualization and downstream analyses (e.g. ChAsE (1), the ChIP-seq web server (http://ccg. vital-it.ch/chipseq), Genomation (2), Homer (3), ngs.plot (4))....
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...ch/chipseq), Genomation (2), Homer (3), ngs....
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8,106 citations
5,037 citations
"deepTools2: a next generation web s..." refers background in this paper
...Since deepTools employ a high level of parallelization for the computationally most expensive tasks, they are well suited to work with a large number of samples emerging from large-scale data production centers (12,13) or single-cell sequencing (14)....
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