The methods of this recent paper have a lot of manual transformations required. Pipelines are usually more common when a method becomes more established. My guess is that not that much high quality Hi-C data has been generated by enough different labs that everyone just does their own thing.

Using ChIP-seq data you may find evidence for loops as reported by Liang, J et a. (2014), but you can hardly know the actual loop pairs. For RNA-seq data I haven't heard of a method. As for Hi-C there is no consensus on what exactly a loop is. In the papers from Liberman Aiden([1], [2]), loops are defined as CTCF pairs that result in a noticeable enrichment of contacts with respect to background. However, to detect this type of loops a particular method of Hi-C, called In-situ Hi-C, is required, otherwise the signal is very faing. There are other methods to detect contact enrichments that work by identifying pairs of genomic loci that share an enriched number of Hi-C contacts with respect to a background as for example [3], [4]. To identify loops also 4C is commonly used.