Description: Loop analysis makes qualitative predictions of variable change in a system of causally interdependent variables, where "qualitative" means sign only (i.e. increases, decreases, non change, and ambiguous). This implementation includes output support for graphs in .dot file format for use with visualization software such as 'graphviz' (<http://graphviz.org>). 'LoopAnalyst' provides tools for the construction and output of community matrices, computation and output of community effect matrices, tables of correlations, adjoint, absolute feedback, weighted feedback and weighted prediction matrices, change in life expectancy matrices, and feedback, path and loop enumeration tools.

Title: Comprehensive Feedback Loop Detection in ODE Models
Authors@R: c(person("Katharina", "Baum", email = "katharina.baum@hpi.de",
person("Sandra", "Krüger", role = c("ctb")))
Description: Detect feedback loops (cycles, circuits) between species (nodes) in ordinary differential equation (ODE) models. Feedback loops are paths from a node to itself without visiting any other node twice, and they have important regulatory functions. Loops are reported with their order of participating nodes and their length, and whether the loop is a positive or a negative feedback loop. An upper limit of the number of feedback loops limits runtime (which scales with feedback loop count). Model parametrizations and values of the modelled variables are accounted for. Computation uses the characteristics of the Jacobian matrix as described e.g. in Thomas and Kaufman (2002) <doi:10.1016/s1631-0691(02)01452-x>. Input can be the Jacobian matrix of the ODE model or the ODE function definition; in the latter case, the Jacobian matrix is determined using 'numDeriv'. Graph-based algorithms from 'igraph' are employed for path detection.
Suggests: deSolve, knitr, markdown, remotes, rmarkdown, utils
Author: Katharina Baum [aut, cre] (<https://orcid.org/0000-0001-7256-0566>),

Title: Integration and Analysis of Chromatin Loop Data
Authors@R: person("Hassaan Maan", role = c("aut", "cre"),
Description: Common coordinate-based workflows involving processed chromatin loop and genomic element data are considered and packaged into appropriate customizable functions. Includes methods for linking element sets via chromatin loops and creating consensus loop datasets.
Imports: GenomicRanges, IRanges, utils, S4Vectors