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Citrus: Editing HiC data for de novo genome assembly
juicer and 3D-DNA are two tools that re-arranges HiC data (xxx.hic format) and splits/re-orders super-scaffold data (xxx.assembly) to improve de novo genome assembly. Juicebox was specifically designed to tune or adjust genomic sequences based on HiC data. However, the current Juicebox version does not have a function to save updated HiC data and to summarize chromosome sequences. Thus, we created Citrus which can edit super-scaffolds according to chromatin conformation data captured in xxx.hic...
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The Citrus project aims at collecting all the code for cancer systems biology developed by the Califano Lab. Including: ARACNe, pARACNe, DIGGIT and CINDy.
To make it easier to test my app (and hoping to get some real feedback
To make it easier to test my app (and hoping to get some real feedback about it) I created a custom Citrus Perl distribution that includes Tpda3, only for GNU/Linux for now.
So, if you are not afraid of the command line and older technologies (PerlTk),
please, download, install and test my app:
Open a terminal:
% cd test # or any other playground dir
% tar xaf ~/downloads/tpda3perl-standard-51402-20903-linux-x86-061.tar.gz
% cd Tpda3Perl
% ./bin/citrusutils
After exit:
% source bin...
citrusdb is the open source customer care and billing software that can be used in many service industries, internet service, subscriptions, consulting, and telecommunications. Provides CRM, Ticketing, Invoicing, and Credit Card Batches.
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