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@@ -1,8 +1,12 @@
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[](http://bioconda.github.io/recipes/r-calder2/README.html)
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+[](https://hub.docker.com/r/lucananni93/calder2)
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+[](https://www.nextflow.io/)
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+[](https://nf-co.re/modules/calder2)
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# CALDER user manual
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-CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hierarchical organization and obtain sub-compartments; (3) compute nested sub-domains within each chromatin domain from short-range contacts. CALDER is currently implemented in R.
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+CALDER is a Hi-C analysis tool that allows: (1) compute chromatin dom
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+ains from whole chromosome contacts; (2) derive their non-linear hierarchical organization and obtain sub-compartments; (3) compute nested sub-domains within each chromatin domain from short-range contacts. CALDER is currently implemented in R.
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* Overview of the CALDER method:
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@@ -23,6 +27,7 @@ Below we introduce two main updates:
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### (1) Optimized `bin_size` selection
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+
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Due to reasons such as low data quality or large scale structural variation, compartments can be unreliably called at one `bin_size` (equivalent to `resolution` in the literature) but properly called at another `bin_size`. We added an optimized `bin_size` selection strategy to call reliable compartments. This strategy is based on the observation from our large scale compartment analysis (https://www.nature.com/articles/s41467-021-22666-3), that although compartments can change between different conditions, their overall correlation `cor(compartment_rank_1, compartment_rank_2)` is high (> 0.4).
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<br>
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<br>
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@@ -98,6 +103,25 @@ remotes::install_github("CSOgroup/CALDER2.0")
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Please contact yliueagle@googlemail.com for any questions about installation.
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+## Use as a docker container
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+We provide a [Docker image](https://hub.docker.com/r/lucananni93/calder2) complete with all dependencies to run CALDER workflows.
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+
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+```
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+# Pull the docker image from Dockerhub
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+docker pull lucananni93/calder2
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+
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+# Run the image
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+docker run -it lucananni93/calder2
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+
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+# Once inside the image we can run the command line Calder tool
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+calder [options]
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+
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+# or we can just enter R
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+R
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+
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+# and load Calder
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+library(CALDER)
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+```
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# Usage
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