Biomedical Engineering Reference
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(4) permutation_test for enrichment analyses. Additionally, in this
distribution, we are including auxiliary tools for manipulating vectors
and matrices.
The fl ow-chart in Figure 8.2 summarizes the role of each of the
command-line tools in our pipeline model. Briefl y, the pipeline inputs in
REG/GFF/BED/SAM format represent either sequenced read alignments
(e.g. from DNA-seq, RNA-seq, ChIP-seq experiments) or annotations
from public databases. The annotations that can be utilized in our
pipeline fall into two categories: (1) genomic annotations represented as
genomic regions, such as the known genes set in the UCSC Genome
Browser; and (2) functional annotations, for example from Gene
Ontology [29]. Computations are performed in two levels: (1) basic
interval operations (such as unions, intersections, shifting, fl anking, etc.)
are implemented by the genomic_regions command-line tool; and (2)
complex operations (overlaps, offsets, scanning and permutations)
implemented by the genomic_overlaps, genomic_scans and permutation_
test command-line tools take as input the regions that have undergone
basic processing and produce results. Basic and complex operations
Flow-chart describing the various functionalities of the
GenomicTools suite: basic region operations are
implemented in genomic_regions whereas complex
operations are implemented in genomic_overlaps,
genomic_scans and permutation_test (source: adapted
fi gure 1 from Tsirigos et al. [20])
Figure 8.2
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