TransCistor

TransCistor is an analytical framework which aims to classify cis- or trans-acting long non-coding RNAs(lncRNAs). It includes two modules; digital and analogue. There is only one file required as input: a processed whole-transcriptome list of target/not-target genes (“regulation file”).
https://www.biorxiv.org/content/10.1101/2022.09.18.508380v1

Description

TransCistor-digital tests for statistical enrichment in proximal genes using the hypergeometric distribution. Proximity is defined based on Topologically Associating Domains (TADs).

TransCistor-analogue, defines a distance statistic as the mean TSS-to-TSS distance of all same-chromosome targets of a given lncRNA. To estimate statistical significance, a null distribution is calculated by randomisation of target labels.

Getting Started

Dependencies

TransCistor is built as a webserver (https://transcistor.unibe.ch/) or a standalone script.
* The webserver is a shiny app and has no dependencies.
* The standalone version is built in R and the main dependencies are R packages: tidyverse, dplyr, rlang, rlist, etc.

Executing/Installing TransCistor

* For single-case studies we highly recommend to use the webserver version of TransCistor (https://transcistor.unibe.ch/). 
* Standalone version is recommended for analysing multiple datasets. Executing simply requires the start_TransCistor.R script. The tested dataset can be changed by manipulating the metadata and RegulationFiles directory

``` 
TransCistor <- function(input.file, id.type, species, TAD='All',
                        lncRNA.name, lncRNA.chr, lncRNA.tss, lncRNA.strand = "+", simulations = 100000 )
```